- Presentation: lcolladotor.github.io/derTutor/
- R code: lcolladotor.github.io/derTutor/index.R
December 9th, 2014
Pre-reqs
This is a short tutorial on how to use derfinder (Collado-Torres, Frazee, Jaffe, and Leek, 2014).
In order to run this tutorial, you will need R 3.1.2 or newer (available from CRAN) and derfinder which is available from Bioconductor. It can be installed by:
## Install derfinder from BioC
source('http://bioconductor.org/biocLite.R')
biocLite('derfinder')
You will also need TxDb.Hsapiens.UCSC.hg19.knownGene
biocLite('TxDb.Hsapiens.UCSC.hg19.knownGene')
Docs
You can find the latest documentation at
- Intro to derfinder vignette
- Advanced details and usage vignette
- derfinderPlot
- regionReport
- help pages
help(package = 'derfinder')
Coming soon:
derfinderpaper
Why should I use derfinder?
- You want to perform differential expression analysis at base-pair resolution
- Because it's annotation-agnostic
- Can handle your data set (has been used with ~500 samples)
- Others have gotten grants partially thanks to it
What will I need?
- Most likely a high performance computing environment. It'll depend on the size of your data set
- Familiarity with other packages such as GenomicRanges
- Experience writing
bashscripts can help, although its not required
What does it do?
- It calculates F-statistics at every base: uses nested models
- Let \(y_{ij} = \log_2\left( \text{coverage}_{ij} + \text{scaling factor} \right)\) for position \(i\) and sample \(j\)
- Alternative model: \[ y_{ij} = \alpha_i + \sum_{p=1}^n \beta_{ip} X_{jp} + \sum_{q=1}^m \gamma_{iq} Z_{jq} + \epsilon_{ij} \]
- Null model doesn't have \(\beta\) terms.
- F-statistics are given by: \[ F_i = \frac{(\text{RSS}0_i - \text{RSS}1_i) / (\text{df}_1 - \text{df}_0) }{ \text{offset} + (\text{RSS}1_i / (n - \text{df}_1)) } \]
Main functions
Finding DERs
Data
Simulated data using polyester (Jaffe, Frazee, and Leek, 2014) for 3 groups, 10 samples per group, fold changes 2x and \(\frac{1}{2}\)x.
- 24 single transcript genes
- 12 set to be DE: 4 per group (2 high, 2 low, other groups normal)
- 12 not DE
- 36 two transcript genes
- 12 not DE
- 12 one transcript DE
- 12 both transcripts DE
Aligned with TopHat 2.0.13. Saved coverage in BigWig files.
Load data
library('derfinder')
library('TxDb.Hsapiens.UCSC.hg19.knownGene')
## Files
files <- paste0('http://lcolladotor.github.io/derTutor/data/sample',
1:30, '.bw')
names(files) <- paste0('sample', 1:30)
## Load data
system.time( fullCov <- fullCoverage(files, 'chr22', verbose = FALSE) )
## user system elapsed ## 4.862 0.087 9.348
## You are using Windows? # Use http://lcolladotor.github.io/derTutor/data/fullCov.Rdata
Lib size
## Calculate library size adjustment system.time( collapsedFull <- collapseFullCoverage(fullCov) )
## user system elapsed ## 5.290 0.115 5.411
lapply(collapsedFull[[1]], head)
## $values ## [1] 0 1 2 3 4 5 ## ## $weights ## [1] 51191562 441 300 196 159 209
sampleDepths <- sampleDepth(collapsedFull, probs = 1)
## 2014-12-09 10:56:08 sampleDepth: Calculating sample quantiles ## 2014-12-09 10:56:08 sampleDepth: Calculating sample adjustments
Build models
## Create models
groupInfo <- factor(rep(c('A', 'B', 'C'), each = 10))
models <- makeModels(sampleDepths = sampleDepths, testvars = groupInfo)
Run analysis
## Filter Data covData <- filterData(fullCov$chr22, cutoff = 0)
## 2014-12-09 10:56:09 filterData: originally there were 51304566 rows, now there are 114584 rows. Meaning that 99.78 percent was filtered.
## Run analysis for chr22
dir.create('chr22', showWarnings = FALSE)
system.time(
res <- analyzeChr(chr = 'chr22', coverageInfo = covData, models = models,
cutoffFstat = 1e-03, cutoffPre = 0,
nPermute = 100, seeds = seq_len(100) + 20141202, maxClusterGap = 3000,
groupInfo = groupInfo, mc.cores = 1,
lowMemDir = file.path(tempdir(), 'chr22', 'chunksDir'),
writeOutput = TRUE, returnOutput = TRUE)
)
## 2014-12-09 10:56:09 analyzeChr: Pre-processing the coverage data ## 2014-12-09 10:56:21 analyzeChr: Calculating statistics ## 2014-12-09 10:56:21 calculateStats: calculating the F-statistics ## 2014-12-09 10:56:22 analyzeChr: Calculating pvalues ## 2014-12-09 10:56:22 analyzeChr: Using the following theoretical cutoff for the F-statistics 9.11630563808366 ## 2014-12-09 10:56:22 calculatePvalues: identifying data segments ## 2014-12-09 10:56:22 findRegions: segmenting F-stats information ## 2014-12-09 10:56:22 findRegions: identifying candidate regions ## 2014-12-09 10:56:22 findRegions: identifying region clusters ## 2014-12-09 10:56:22 calculatePvalues: calculating F-statistics for permutation 1 and seed 20141203 ## 2014-12-09 10:56:23 findRegions: segmenting F-stats information ## 2014-12-09 10:56:23 findRegions: identifying candidate regions ## 2014-12-09 10:56:23 calculatePvalues: calculating F-statistics for permutation 2 and seed 20141204 ## 2014-12-09 10:56:24 findRegions: segmenting F-stats information ## 2014-12-09 10:56:24 findRegions: identifying candidate regions ## 2014-12-09 10:56:24 calculatePvalues: calculating F-statistics for permutation 3 and seed 20141205 ## 2014-12-09 10:56:25 findRegions: segmenting F-stats information ## 2014-12-09 10:56:25 findRegions: identifying candidate regions ## 2014-12-09 10:56:25 calculatePvalues: calculating F-statistics for permutation 4 and seed 20141206 ## 2014-12-09 10:56:26 findRegions: segmenting F-stats information ## 2014-12-09 10:56:26 findRegions: identifying candidate regions ## 2014-12-09 10:56:26 calculatePvalues: calculating F-statistics for permutation 5 and seed 20141207 ## 2014-12-09 10:56:26 findRegions: segmenting F-stats information ## 2014-12-09 10:56:26 findRegions: identifying candidate regions ## 2014-12-09 10:56:26 calculatePvalues: calculating F-statistics for permutation 6 and seed 20141208 ## 2014-12-09 10:56:27 findRegions: segmenting F-stats information ## 2014-12-09 10:56:27 findRegions: identifying candidate regions ## 2014-12-09 10:56:27 calculatePvalues: calculating F-statistics for permutation 7 and seed 20141209 ## 2014-12-09 10:56:28 findRegions: segmenting F-stats information ## 2014-12-09 10:56:28 findRegions: identifying candidate regions ## 2014-12-09 10:56:28 calculatePvalues: calculating F-statistics for permutation 8 and seed 20141210 ## 2014-12-09 10:56:28 findRegions: segmenting F-stats information ## 2014-12-09 10:56:28 findRegions: identifying candidate regions ## 2014-12-09 10:56:28 calculatePvalues: calculating F-statistics for permutation 9 and seed 20141211 ## 2014-12-09 10:56:29 findRegions: segmenting F-stats information ## 2014-12-09 10:56:29 findRegions: identifying candidate regions ## 2014-12-09 10:56:29 calculatePvalues: calculating F-statistics for permutation 10 and seed 20141212 ## 2014-12-09 10:56:30 findRegions: segmenting F-stats information ## 2014-12-09 10:56:30 findRegions: identifying candidate regions ## 2014-12-09 10:56:30 calculatePvalues: calculating F-statistics for permutation 11 and seed 20141213 ## 2014-12-09 10:56:31 findRegions: segmenting F-stats information ## 2014-12-09 10:56:31 findRegions: identifying candidate regions ## 2014-12-09 10:56:31 calculatePvalues: calculating F-statistics for permutation 12 and seed 20141214 ## 2014-12-09 10:56:31 findRegions: segmenting F-stats information ## 2014-12-09 10:56:31 findRegions: identifying candidate regions ## 2014-12-09 10:56:31 calculatePvalues: calculating F-statistics for permutation 13 and seed 20141215 ## 2014-12-09 10:56:32 findRegions: segmenting F-stats information ## 2014-12-09 10:56:32 findRegions: identifying candidate regions ## 2014-12-09 10:56:32 calculatePvalues: calculating F-statistics for permutation 14 and seed 20141216 ## 2014-12-09 10:56:33 findRegions: segmenting F-stats information ## 2014-12-09 10:56:33 findRegions: identifying candidate regions ## 2014-12-09 10:56:33 calculatePvalues: calculating F-statistics for permutation 15 and seed 20141217 ## 2014-12-09 10:56:33 findRegions: segmenting F-stats information ## 2014-12-09 10:56:34 findRegions: identifying candidate regions ## 2014-12-09 10:56:34 calculatePvalues: calculating F-statistics for permutation 16 and seed 20141218 ## 2014-12-09 10:56:34 findRegions: segmenting F-stats information ## 2014-12-09 10:56:34 findRegions: identifying candidate regions ## 2014-12-09 10:56:34 calculatePvalues: calculating F-statistics for permutation 17 and seed 20141219 ## 2014-12-09 10:56:35 findRegions: segmenting F-stats information ## 2014-12-09 10:56:35 findRegions: identifying candidate regions ## 2014-12-09 10:56:35 calculatePvalues: calculating F-statistics for permutation 18 and seed 20141220 ## 2014-12-09 10:56:36 findRegions: segmenting F-stats information ## 2014-12-09 10:56:36 findRegions: identifying candidate regions ## 2014-12-09 10:56:36 calculatePvalues: calculating F-statistics for permutation 19 and seed 20141221 ## 2014-12-09 10:56:36 findRegions: segmenting F-stats information ## 2014-12-09 10:56:36 findRegions: identifying candidate regions ## 2014-12-09 10:56:36 calculatePvalues: calculating F-statistics for permutation 20 and seed 20141222 ## 2014-12-09 10:56:37 findRegions: segmenting F-stats information ## 2014-12-09 10:56:37 findRegions: identifying candidate regions ## 2014-12-09 10:56:37 calculatePvalues: calculating F-statistics for permutation 21 and seed 20141223 ## 2014-12-09 10:56:38 findRegions: segmenting F-stats information ## 2014-12-09 10:56:38 findRegions: identifying candidate regions ## 2014-12-09 10:56:38 calculatePvalues: calculating F-statistics for permutation 22 and seed 20141224 ## 2014-12-09 10:56:39 findRegions: segmenting F-stats information ## 2014-12-09 10:56:39 findRegions: identifying candidate regions ## 2014-12-09 10:56:39 calculatePvalues: calculating F-statistics for permutation 23 and seed 20141225 ## 2014-12-09 10:56:40 findRegions: segmenting F-stats information ## 2014-12-09 10:56:40 findRegions: identifying candidate regions ## 2014-12-09 10:56:40 calculatePvalues: calculating F-statistics for permutation 24 and seed 20141226 ## 2014-12-09 10:56:40 findRegions: segmenting F-stats information ## 2014-12-09 10:56:40 findRegions: identifying candidate regions ## 2014-12-09 10:56:40 calculatePvalues: calculating F-statistics for permutation 25 and seed 20141227 ## 2014-12-09 10:56:41 findRegions: segmenting F-stats information ## 2014-12-09 10:56:41 findRegions: identifying candidate regions ## 2014-12-09 10:56:41 calculatePvalues: calculating F-statistics for permutation 26 and seed 20141228 ## 2014-12-09 10:56:42 findRegions: segmenting F-stats information ## 2014-12-09 10:56:42 findRegions: identifying candidate regions ## 2014-12-09 10:56:42 calculatePvalues: calculating F-statistics for permutation 27 and seed 20141229 ## 2014-12-09 10:56:43 findRegions: segmenting F-stats information ## 2014-12-09 10:56:43 findRegions: identifying candidate regions ## 2014-12-09 10:56:43 calculatePvalues: calculating F-statistics for permutation 28 and seed 20141230 ## 2014-12-09 10:56:44 findRegions: segmenting F-stats information ## 2014-12-09 10:56:44 findRegions: identifying candidate regions ## 2014-12-09 10:56:44 calculatePvalues: calculating F-statistics for permutation 29 and seed 20141231 ## 2014-12-09 10:56:45 findRegions: segmenting F-stats information ## 2014-12-09 10:56:45 findRegions: identifying candidate regions ## 2014-12-09 10:56:45 calculatePvalues: calculating F-statistics for permutation 30 and seed 20141232 ## 2014-12-09 10:56:45 findRegions: segmenting F-stats information ## 2014-12-09 10:56:45 findRegions: identifying candidate regions ## 2014-12-09 10:56:45 calculatePvalues: calculating F-statistics for permutation 31 and seed 20141233 ## 2014-12-09 10:56:46 findRegions: segmenting F-stats information ## 2014-12-09 10:56:46 findRegions: identifying candidate regions ## 2014-12-09 10:56:46 calculatePvalues: calculating F-statistics for permutation 32 and seed 20141234 ## 2014-12-09 10:56:47 findRegions: segmenting F-stats information ## 2014-12-09 10:56:47 findRegions: identifying candidate regions ## 2014-12-09 10:56:47 calculatePvalues: calculating F-statistics for permutation 33 and seed 20141235 ## 2014-12-09 10:56:48 findRegions: segmenting F-stats information ## 2014-12-09 10:56:48 findRegions: identifying candidate regions ## 2014-12-09 10:56:48 calculatePvalues: calculating F-statistics for permutation 34 and seed 20141236 ## 2014-12-09 10:56:49 findRegions: segmenting F-stats information ## 2014-12-09 10:56:49 findRegions: identifying candidate regions ## 2014-12-09 10:56:49 calculatePvalues: calculating F-statistics for permutation 35 and seed 20141237 ## 2014-12-09 10:56:50 findRegions: segmenting F-stats information ## 2014-12-09 10:56:50 findRegions: identifying candidate regions ## 2014-12-09 10:56:50 calculatePvalues: calculating F-statistics for permutation 36 and seed 20141238 ## 2014-12-09 10:56:51 findRegions: segmenting F-stats information ## 2014-12-09 10:56:51 findRegions: identifying candidate regions ## 2014-12-09 10:56:51 calculatePvalues: calculating F-statistics for permutation 37 and seed 20141239 ## 2014-12-09 10:56:52 findRegions: segmenting F-stats information ## 2014-12-09 10:56:52 findRegions: identifying candidate regions ## 2014-12-09 10:56:52 calculatePvalues: calculating F-statistics for permutation 38 and seed 20141240 ## 2014-12-09 10:56:53 findRegions: segmenting F-stats information ## 2014-12-09 10:56:53 findRegions: identifying candidate regions ## 2014-12-09 10:56:53 calculatePvalues: calculating F-statistics for permutation 39 and seed 20141241 ## 2014-12-09 10:56:54 findRegions: segmenting F-stats information ## 2014-12-09 10:56:54 findRegions: identifying candidate regions ## 2014-12-09 10:56:54 calculatePvalues: calculating F-statistics for permutation 40 and seed 20141242 ## 2014-12-09 10:56:55 findRegions: segmenting F-stats information ## 2014-12-09 10:56:55 findRegions: identifying candidate regions ## 2014-12-09 10:56:55 calculatePvalues: calculating F-statistics for permutation 41 and seed 20141243 ## 2014-12-09 10:56:56 findRegions: segmenting F-stats information ## 2014-12-09 10:56:56 findRegions: identifying candidate regions ## 2014-12-09 10:56:56 calculatePvalues: calculating F-statistics for permutation 42 and seed 20141244 ## 2014-12-09 10:56:57 findRegions: segmenting F-stats information ## 2014-12-09 10:56:57 findRegions: identifying candidate regions ## 2014-12-09 10:56:57 calculatePvalues: calculating F-statistics for permutation 43 and seed 20141245 ## 2014-12-09 10:56:58 findRegions: segmenting F-stats information ## 2014-12-09 10:56:58 findRegions: identifying candidate regions ## 2014-12-09 10:56:58 calculatePvalues: calculating F-statistics for permutation 44 and seed 20141246 ## 2014-12-09 10:56:59 findRegions: segmenting F-stats information ## 2014-12-09 10:56:59 findRegions: identifying candidate regions ## 2014-12-09 10:56:59 calculatePvalues: calculating F-statistics for permutation 45 and seed 20141247 ## 2014-12-09 10:57:00 findRegions: segmenting F-stats information ## 2014-12-09 10:57:00 findRegions: identifying candidate regions ## 2014-12-09 10:57:00 calculatePvalues: calculating F-statistics for permutation 46 and seed 20141248 ## 2014-12-09 10:57:01 findRegions: segmenting F-stats information ## 2014-12-09 10:57:01 findRegions: identifying candidate regions ## 2014-12-09 10:57:01 calculatePvalues: calculating F-statistics for permutation 47 and seed 20141249 ## 2014-12-09 10:57:02 findRegions: segmenting F-stats information ## 2014-12-09 10:57:02 findRegions: identifying candidate regions ## 2014-12-09 10:57:02 calculatePvalues: calculating F-statistics for permutation 48 and seed 20141250 ## 2014-12-09 10:57:03 findRegions: segmenting F-stats information ## 2014-12-09 10:57:03 findRegions: identifying candidate regions ## 2014-12-09 10:57:03 calculatePvalues: calculating F-statistics for permutation 49 and seed 20141251 ## 2014-12-09 10:57:04 findRegions: segmenting F-stats information ## 2014-12-09 10:57:04 findRegions: identifying candidate regions ## 2014-12-09 10:57:04 calculatePvalues: calculating F-statistics for permutation 50 and seed 20141252 ## 2014-12-09 10:57:05 findRegions: segmenting F-stats information ## 2014-12-09 10:57:05 findRegions: identifying candidate regions ## 2014-12-09 10:57:05 calculatePvalues: calculating F-statistics for permutation 51 and seed 20141253 ## 2014-12-09 10:57:05 findRegions: segmenting F-stats information ## 2014-12-09 10:57:05 findRegions: identifying candidate regions ## 2014-12-09 10:57:05 calculatePvalues: calculating F-statistics for permutation 52 and seed 20141254 ## 2014-12-09 10:57:06 findRegions: segmenting F-stats information ## 2014-12-09 10:57:06 findRegions: identifying candidate regions ## 2014-12-09 10:57:06 calculatePvalues: calculating F-statistics for permutation 53 and seed 20141255 ## 2014-12-09 10:57:07 findRegions: segmenting F-stats information ## 2014-12-09 10:57:07 findRegions: identifying candidate regions ## 2014-12-09 10:57:07 calculatePvalues: calculating F-statistics for permutation 54 and seed 20141256 ## 2014-12-09 10:57:07 findRegions: segmenting F-stats information ## 2014-12-09 10:57:07 findRegions: identifying candidate regions ## 2014-12-09 10:57:07 calculatePvalues: calculating F-statistics for permutation 55 and seed 20141257 ## 2014-12-09 10:57:08 findRegions: segmenting F-stats information ## 2014-12-09 10:57:08 findRegions: identifying candidate regions ## 2014-12-09 10:57:08 calculatePvalues: calculating F-statistics for permutation 56 and seed 20141258 ## 2014-12-09 10:57:09 findRegions: segmenting F-stats information ## 2014-12-09 10:57:09 findRegions: identifying candidate regions ## 2014-12-09 10:57:09 calculatePvalues: calculating F-statistics for permutation 57 and seed 20141259 ## 2014-12-09 10:57:09 findRegions: segmenting F-stats information ## 2014-12-09 10:57:09 findRegions: identifying candidate regions ## 2014-12-09 10:57:09 calculatePvalues: calculating F-statistics for permutation 58 and seed 20141260 ## 2014-12-09 10:57:10 findRegions: segmenting F-stats information ## 2014-12-09 10:57:10 findRegions: identifying candidate regions ## 2014-12-09 10:57:10 calculatePvalues: calculating F-statistics for permutation 59 and seed 20141261 ## 2014-12-09 10:57:11 findRegions: segmenting F-stats information ## 2014-12-09 10:57:11 findRegions: identifying candidate regions ## 2014-12-09 10:57:11 calculatePvalues: calculating F-statistics for permutation 60 and seed 20141262 ## 2014-12-09 10:57:11 findRegions: segmenting F-stats information ## 2014-12-09 10:57:11 findRegions: identifying candidate regions ## 2014-12-09 10:57:11 calculatePvalues: calculating F-statistics for permutation 61 and seed 20141263 ## 2014-12-09 10:57:12 findRegions: segmenting F-stats information ## 2014-12-09 10:57:12 findRegions: identifying candidate regions ## 2014-12-09 10:57:12 calculatePvalues: calculating F-statistics for permutation 62 and seed 20141264 ## 2014-12-09 10:57:13 findRegions: segmenting F-stats information ## 2014-12-09 10:57:13 findRegions: identifying candidate regions ## 2014-12-09 10:57:13 calculatePvalues: calculating F-statistics for permutation 63 and seed 20141265 ## 2014-12-09 10:57:14 findRegions: segmenting F-stats information ## 2014-12-09 10:57:14 findRegions: identifying candidate regions ## 2014-12-09 10:57:14 calculatePvalues: calculating F-statistics for permutation 64 and seed 20141266 ## 2014-12-09 10:57:15 findRegions: segmenting F-stats information ## 2014-12-09 10:57:15 findRegions: identifying candidate regions ## 2014-12-09 10:57:15 calculatePvalues: calculating F-statistics for permutation 65 and seed 20141267 ## 2014-12-09 10:57:15 findRegions: segmenting F-stats information ## 2014-12-09 10:57:15 findRegions: identifying candidate regions ## 2014-12-09 10:57:15 calculatePvalues: calculating F-statistics for permutation 66 and seed 20141268 ## 2014-12-09 10:57:16 findRegions: segmenting F-stats information ## 2014-12-09 10:57:16 findRegions: identifying candidate regions ## 2014-12-09 10:57:16 calculatePvalues: calculating F-statistics for permutation 67 and seed 20141269 ## 2014-12-09 10:57:17 findRegions: segmenting F-stats information ## 2014-12-09 10:57:17 findRegions: identifying candidate regions ## 2014-12-09 10:57:17 calculatePvalues: calculating F-statistics for permutation 68 and seed 20141270 ## 2014-12-09 10:57:17 findRegions: segmenting F-stats information ## 2014-12-09 10:57:17 findRegions: identifying candidate regions ## 2014-12-09 10:57:17 calculatePvalues: calculating F-statistics for permutation 69 and seed 20141271 ## 2014-12-09 10:57:18 findRegions: segmenting F-stats information ## 2014-12-09 10:57:18 findRegions: identifying candidate regions ## 2014-12-09 10:57:18 calculatePvalues: calculating F-statistics for permutation 70 and seed 20141272 ## 2014-12-09 10:57:19 findRegions: segmenting F-stats information ## 2014-12-09 10:57:19 findRegions: identifying candidate regions ## 2014-12-09 10:57:19 calculatePvalues: calculating F-statistics for permutation 71 and seed 20141273 ## 2014-12-09 10:57:19 findRegions: segmenting F-stats information ## 2014-12-09 10:57:19 findRegions: identifying candidate regions ## 2014-12-09 10:57:19 calculatePvalues: calculating F-statistics for permutation 72 and seed 20141274 ## 2014-12-09 10:57:20 findRegions: segmenting F-stats information ## 2014-12-09 10:57:20 findRegions: identifying candidate regions ## 2014-12-09 10:57:20 calculatePvalues: calculating F-statistics for permutation 73 and seed 20141275 ## 2014-12-09 10:57:21 findRegions: segmenting F-stats information ## 2014-12-09 10:57:21 findRegions: identifying candidate regions ## 2014-12-09 10:57:21 calculatePvalues: calculating F-statistics for permutation 74 and seed 20141276 ## 2014-12-09 10:57:22 findRegions: segmenting F-stats information ## 2014-12-09 10:57:22 findRegions: identifying candidate regions ## 2014-12-09 10:57:22 calculatePvalues: calculating F-statistics for permutation 75 and seed 20141277 ## 2014-12-09 10:57:22 findRegions: segmenting F-stats information ## 2014-12-09 10:57:22 findRegions: identifying candidate regions ## 2014-12-09 10:57:22 calculatePvalues: calculating F-statistics for permutation 76 and seed 20141278 ## 2014-12-09 10:57:23 findRegions: segmenting F-stats information ## 2014-12-09 10:57:23 findRegions: identifying candidate regions ## 2014-12-09 10:57:23 calculatePvalues: calculating F-statistics for permutation 77 and seed 20141279 ## 2014-12-09 10:57:23 findRegions: segmenting F-stats information ## 2014-12-09 10:57:24 findRegions: identifying candidate regions ## 2014-12-09 10:57:24 calculatePvalues: calculating F-statistics for permutation 78 and seed 20141280 ## 2014-12-09 10:57:24 findRegions: segmenting F-stats information ## 2014-12-09 10:57:24 findRegions: identifying candidate regions ## 2014-12-09 10:57:24 calculatePvalues: calculating F-statistics for permutation 79 and seed 20141281 ## 2014-12-09 10:57:25 findRegions: segmenting F-stats information ## 2014-12-09 10:57:25 findRegions: identifying candidate regions ## 2014-12-09 10:57:25 calculatePvalues: calculating F-statistics for permutation 80 and seed 20141282 ## 2014-12-09 10:57:26 findRegions: segmenting F-stats information ## 2014-12-09 10:57:26 findRegions: identifying candidate regions ## 2014-12-09 10:57:26 calculatePvalues: calculating F-statistics for permutation 81 and seed 20141283 ## 2014-12-09 10:57:26 findRegions: segmenting F-stats information ## 2014-12-09 10:57:26 findRegions: identifying candidate regions ## 2014-12-09 10:57:26 calculatePvalues: calculating F-statistics for permutation 82 and seed 20141284 ## 2014-12-09 10:57:27 findRegions: segmenting F-stats information ## 2014-12-09 10:57:27 findRegions: identifying candidate regions ## 2014-12-09 10:57:27 calculatePvalues: calculating F-statistics for permutation 83 and seed 20141285 ## 2014-12-09 10:57:28 findRegions: segmenting F-stats information ## 2014-12-09 10:57:28 findRegions: identifying candidate regions ## 2014-12-09 10:57:28 calculatePvalues: calculating F-statistics for permutation 84 and seed 20141286 ## 2014-12-09 10:57:28 findRegions: segmenting F-stats information ## 2014-12-09 10:57:28 findRegions: identifying candidate regions ## 2014-12-09 10:57:28 calculatePvalues: calculating F-statistics for permutation 85 and seed 20141287 ## 2014-12-09 10:57:29 findRegions: segmenting F-stats information ## 2014-12-09 10:57:29 findRegions: identifying candidate regions ## 2014-12-09 10:57:29 calculatePvalues: calculating F-statistics for permutation 86 and seed 20141288 ## 2014-12-09 10:57:30 findRegions: segmenting F-stats information ## 2014-12-09 10:57:30 findRegions: identifying candidate regions ## 2014-12-09 10:57:30 calculatePvalues: calculating F-statistics for permutation 87 and seed 20141289 ## 2014-12-09 10:57:31 findRegions: segmenting F-stats information ## 2014-12-09 10:57:31 findRegions: identifying candidate regions ## 2014-12-09 10:57:31 calculatePvalues: calculating F-statistics for permutation 88 and seed 20141290 ## 2014-12-09 10:57:31 findRegions: segmenting F-stats information ## 2014-12-09 10:57:31 findRegions: identifying candidate regions ## 2014-12-09 10:57:31 calculatePvalues: calculating F-statistics for permutation 89 and seed 20141291 ## 2014-12-09 10:57:32 findRegions: segmenting F-stats information ## 2014-12-09 10:57:32 findRegions: identifying candidate regions ## 2014-12-09 10:57:32 calculatePvalues: calculating F-statistics for permutation 90 and seed 20141292 ## 2014-12-09 10:57:33 findRegions: segmenting F-stats information ## 2014-12-09 10:57:33 findRegions: identifying candidate regions ## 2014-12-09 10:57:33 calculatePvalues: calculating F-statistics for permutation 91 and seed 20141293 ## 2014-12-09 10:57:33 findRegions: segmenting F-stats information ## 2014-12-09 10:57:33 findRegions: identifying candidate regions ## 2014-12-09 10:57:33 calculatePvalues: calculating F-statistics for permutation 92 and seed 20141294 ## 2014-12-09 10:57:34 findRegions: segmenting F-stats information ## 2014-12-09 10:57:34 findRegions: identifying candidate regions ## 2014-12-09 10:57:34 calculatePvalues: calculating F-statistics for permutation 93 and seed 20141295 ## 2014-12-09 10:57:35 findRegions: segmenting F-stats information ## 2014-12-09 10:57:35 findRegions: identifying candidate regions ## 2014-12-09 10:57:35 calculatePvalues: calculating F-statistics for permutation 94 and seed 20141296 ## 2014-12-09 10:57:35 findRegions: segmenting F-stats information ## 2014-12-09 10:57:35 findRegions: identifying candidate regions ## 2014-12-09 10:57:35 calculatePvalues: calculating F-statistics for permutation 95 and seed 20141297 ## 2014-12-09 10:57:36 findRegions: segmenting F-stats information ## 2014-12-09 10:57:36 findRegions: identifying candidate regions ## 2014-12-09 10:57:36 calculatePvalues: calculating F-statistics for permutation 96 and seed 20141298 ## 2014-12-09 10:57:37 findRegions: segmenting F-stats information ## 2014-12-09 10:57:37 findRegions: identifying candidate regions ## 2014-12-09 10:57:37 calculatePvalues: calculating F-statistics for permutation 97 and seed 20141299 ## 2014-12-09 10:57:38 findRegions: segmenting F-stats information ## 2014-12-09 10:57:38 findRegions: identifying candidate regions ## 2014-12-09 10:57:38 calculatePvalues: calculating F-statistics for permutation 98 and seed 20141300 ## 2014-12-09 10:57:38 findRegions: segmenting F-stats information ## 2014-12-09 10:57:38 findRegions: identifying candidate regions ## 2014-12-09 10:57:39 calculatePvalues: calculating F-statistics for permutation 99 and seed 20141301 ## 2014-12-09 10:57:39 findRegions: segmenting F-stats information ## 2014-12-09 10:57:39 findRegions: identifying candidate regions ## 2014-12-09 10:57:39 calculatePvalues: calculating F-statistics for permutation 100 and seed 20141302 ## 2014-12-09 10:57:40 findRegions: segmenting F-stats information ## 2014-12-09 10:57:40 findRegions: identifying candidate regions ## 2014-12-09 10:57:40 calculatePvalues: calculating the p-values ## 2014-12-09 10:57:40 analyzeChr: Annotating regions
## Matching regions to genes. ## nearestgene: loading bumphunter hg19 transcript database ## finding nearest transcripts... ## AnnotatingDone.
## user system elapsed ## 101.531 8.735 110.403
Explore results
names(res)
## [1] "timeinfo" "optionsStats" "coveragePrep" "fstats" ## [5] "regions" "annotation"
dir('chr22')
## [1] "annotation.Rdata" "coveragePrep.Rdata" "fstats.Rdata" ## [4] "optionsStats.Rdata" "regions.Rdata" "timeinfo.Rdata"
names(res$coveragePrep)
## [1] "coverageProcessed" "mclapplyIndex" "position" ## [4] "meanCoverage" "groupMeans"
names(res$regions)
## [1] "regions" "nullStats" "nullWidths" "nullPermutation"
Merge
## Genomic state system.time(gs <- makeGenomicState(txdb=TxDb.Hsapiens.UCSC.hg19.knownGene, chrs='chr22'))
## user system elapsed ## 21.116 1.128 22.262
## Merge results from different chrs
mergeResults('chr22', genomicState = gs$fullGenome, optionsStats = res$optionsStats)
## 2014-12-09 10:58:22 mergeResults: Saving options used ## 2014-12-09 10:58:22 Loading chromosome chr22 ## 2014-12-09 10:58:22 mergeResults: calculating FWER ## 2014-12-09 10:58:22 mergeResults: Saving fullNullSummary ## 2014-12-09 10:58:22 mergeResults: Re-calculating the p-values ## 2014-12-09 10:58:22 mergeResults: Saving fullRegions ## 2014-12-09 10:58:23 mergeResults: assigning genomic states ## 2014-12-09 10:58:23 annotateRegions: counting ## 2014-12-09 10:58:23 annotateRegions: annotating ## 2014-12-09 10:58:23 mergeResults: Saving fullAnnotatedRegions ## 2014-12-09 10:58:23 mergeResults: Saving fullFstats ## 2014-12-09 10:58:23 mergeResults: Saving fullTime
Main results
dir(pattern = 'Rdata')
## [1] "fullAnnotatedRegions.Rdata" "fullFstats.Rdata" ## [3] "fullNullSummary.Rdata" "fullRegions.Rdata" ## [5] "fullTime.Rdata" "optionsMerge.Rdata"
load('fullRegions.Rdata')
class(fullRegions)
## [1] "GRanges" ## attr(,"package") ## [1] "GenomicRanges"
length(fullRegions)
## [1] 469
colnames(mcols(fullRegions))
## [1] "value" "area" "indexStart" ## [4] "indexEnd" "cluster" "clusterL" ## [7] "meanCoverage" "meanA" "meanB" ## [10] "meanC" "log2FoldChangeBvsA" "log2FoldChangeCvsA" ## [13] "pvalues" "significant" "qvalues" ## [16] "significantQval" "name" "annotation" ## [19] "description" "region" "distance" ## [22] "subregion" "insidedistance" "exonnumber" ## [25] "nexons" "UTR" "annoStrand" ## [28] "geneL" "codingL" "fwer" ## [31] "significantFWER"
table(fullRegions$significantFWER)
## ## TRUE FALSE ## 122 347
Need help?
- Post in the Bioconductor support site – remember to use the
derfindertag! - If you think you found a bug, please report it on the derfinder GitHub repo
Citing derfinder
## Citation info
citation('derfinder')
## ## Collado-Torres L, Frazee AC, Jaffe AE and Leek JT (2014). ## _derfinder: Annotation-agnostic differential expression analysis ## of RNA-seq data at base-pair resolution_. ## https://github.com/lcolladotor/derfinder - R package version ## 1.1.14, <URL: ## http://www.bioconductor.org/packages/release/bioc/html/derfinder.html>. ## ## Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA and Leek JT ## (2014). "Differential expression analysis of RNA-seq data at ## single-base resolution." _Biostatistics_, *15 (3)*, pp. 413-426. ## <URL: http://dx.doi.org/10.1093/biostatistics/kxt053>, <URL: ## http://biostatistics.oxfordjournals.org/content/15/3/413.long>.
Reproducibility
Code for creating this page
## Create this page
library('rmarkdown')
render('index.Rmd')
## Clean up
file.remove('derTutorRef.bib')
## Extract the R code
library('knitr')
knit('index.Rmd', tangle = TRUE)
Date this tutorial was generated.
## [1] "2014-12-09 10:58:23 EST"
Wallclock time spent running this tutorial.
## Time difference of 2.733 mins
R session information.
## setting value ## version R Under development (unstable) (2014-11-01 r66923) ## system x86_64, darwin10.8.0 ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## tz America/New_York
## package * version date source ## AnnotationDbi * 1.29.10 2014-11-22 Bioconductor ## BiocParallel 1.1.9 2014-11-24 Bioconductor ## bumphunter 1.7.2 2014-11-19 Bioconductor ## derfinder * 1.1.14 2014-11-22 Github (lcolladotor/derfinder@24f9fbb) ## derfinderHelper 1.1.5 2014-11-05 Bioconductor ## GenomeInfoDb * 1.3.7 2014-11-15 Bioconductor ## GenomicAlignments 1.3.14 2014-12-05 Bioconductor ## GenomicFeatures * 1.19.6 2014-11-04 Bioconductor ## GenomicFiles 1.3.8 2014-11-12 Bioconductor ## GenomicRanges * 1.19.20 2014-12-05 Bioconductor ## Hmisc 3.14.5 2014-09-12 CRAN (R 3.2.0) ## IRanges * 2.1.28 2014-12-05 Bioconductor ## knitcitations * 1.0.4 2014-11-03 Github (cboettig/knitcitations@508de74) ## Matrix 1.1.4 2014-06-15 CRAN (R 3.2.0) ## qvalue 1.41.0 2014-10-14 Bioconductor ## rmarkdown * 0.3.3 2014-09-17 CRAN (R 3.2.0) ## Rsamtools 1.19.11 2014-11-26 Bioconductor ## rtracklayer 1.27.6 2014-11-26 Bioconductor ## S4Vectors * 0.5.14 2014-12-05 Bioconductor ## TxDb.Hsapiens.UCSC.hg19.knownGene * 3.0.0 2014-09-26 Bioconductor
Bibliography
This tutorial was generated using rmarkdown (Allaire, McPherson, Xie, Wickham, et al., 2014) and knitcitations (Boettiger, 2014).
[1] J. Allaire, J. McPherson, Y. Xie, H. Wickham, et al. rmarkdown: Dynamic Documents for R. R package version 0.3.3. 2014. URL: http://CRAN.R-project.org/package=rmarkdown.
[2] C. Boettiger. knitcitations: Citations for knitr markdown files. R package version 1.0.4. 2014. URL: https://github.com/cboettig/knitcitations.
[3] L. Collado-Torres, A. C. Frazee, A. E. Jaffe and J. T. Leek. derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution. https://github.com/lcolladotor/derfinder - R package version 1.1.14. 2014. URL: http://www.bioconductor.org/packages/release/bioc/html/derfinder.html.
[4] A. Jaffe, A. Frazee and J. Leek. polyester: Simulate RNA-seq reads. R package version 1.1.0. 2014.