analyzeChr: Run the derfinder analysis on a chromosome

In lcolladotor/derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

Run the derfinder analysis on a chromosome

Description

This is a major wrapper for running several key functions from this package. It is meant to be used after loadCoverage has been used for a specific chromosome. The steps run include makeModels, preprocessCoverage, calculateStats, calculatePvalues and annotating with annotateTranscripts and matchGenes.

Usage

analyzeChr(
  chr,
  coverageInfo,
  models,
  cutoffPre = 5,
  cutoffFstat = 1e-08,
  cutoffType = "theoretical",
  nPermute = 1,
  seeds = as.integer(gsub("-", "", Sys.Date())) + seq_len(nPermute),
  groupInfo,
  txdb = NULL,
  writeOutput = TRUE,
  runAnnotation = TRUE,
  lowMemDir = file.path(chr, "chunksDir"),
  smooth = FALSE,
  weights = NULL,
  smoothFunction = bumphunter::locfitByCluster,
  ...
)

Arguments

chr	Used for naming the output files when writeOutput=TRUE and the resulting GRanges object.
coverageInfo	A list containing a DataFrame –⁠$coverage⁠– with the coverage data and a logical Rle –⁠$position⁠– with the positions that passed the cutoff. This object is generated using loadCoverage. You should have specified a cutoff value for loadCoverage unless that you are using colsubset which will force a filtering step with filterData when running preprocessCoverage.
models	The output from makeModels.
cutoffPre	This argument is passed to preprocessCoverage (cutoff).
cutoffFstat	This is used to determine the cutoff argument of calculatePvalues and it's behaviour is determined by cutoffType.
cutoffType	If set to empirical, the cutoffFstat (example: 0.99) quantile is used via quantile. If set to theoretical, the theoretical cutoffFstats (example: 1e-08) is calculated via qf. If set to manual, cutoffFstats is passed to calculatePvalues without any other calculation.
nPermute	The number of permutations. Note that for a full chromosome, a small amount (10) of permutations is sufficient. If set to 0, no permutations are performed and thus no null regions are used, however, the ⁠$regions⁠ component is created.
seeds	An integer vector of length nPermute specifying the seeds to be used for each permutation. If NULL no seeds are used.
groupInfo	A factor specifying the group membership of each sample that can later be used with the plotting functions in the derfinderPlot package.
txdb	This argument is passed to annotateTranscripts. If NULL, TxDb.Hsapiens.UCSC.hg19.knownGene is used.
writeOutput	If TRUE, output Rdata files are created at each step inside a directory with the chromosome name (example: 'chr21' if chrnum='21'). One Rdata file is created for each component described in the return section.
runAnnotation	If TRUE annotateTranscripts and matchGenes are run. Otherwise these steps are skipped.
lowMemDir	If specified, each chunk is saved into a separate Rdata file under lowMemDir and later loaded in fstats.apply when running calculateStats and calculatePvalues. Using this option helps reduce the memory load as each fork in bplapply loads only the data needed for the chunk processing. The downside is a bit longer computation time due to input/output.
smooth	Whether to smooth the F-statistics (fstats) or not. This is by default FALSE. For RNA-seq data we recommend using FALSE.
weights	Weights used by the smoother as described in smoother.
smoothFunction	A function to be used for smoothing the F-statistics. Two functions are provided by the bumphunter package: loessByCluster and runmedByCluster. If you are using your own custom function, it has to return a named list with an element called ⁠$fitted⁠ that contains the smoothed F-statistics and an element claled ⁠$smoothed⁠ that is a logical vector indicating whether the F-statistics were smoothed or not. If they are not smoothed, the original values will be used.
...	Arguments passed to other methods and/or advanced arguments. Advanced arguments: verbose If TRUE basic status updates will be printed along the way. Default TRUE. scalefac This argument is passed to preprocessCoverage. chunksize This argument is passed to preprocessCoverage. returnOutput If TRUE, it returns a list with the results from each step. Otherwise, it returns NULL. Default: the opposite of writeOutput. Passed to extendedMapSeqlevels, preprocessCoverage, calculateStats, calculatePvalues, annotateTranscripts, matchGenes, and define_cluster.

Details

If you are working with data from an organism different from 'Homo sapiens' specify so by setting the global 'species' and 'chrsStyle' options. For example: options(species = 'arabidopsis_thaliana') options(chrsStyle = 'NCBI')

Value

If returnOutput=TRUE, a list with six components:

timeinfo

The wallclock timing information for each step.

optionsStats

The main options used when running this function.

coveragePrep

The output from preprocessCoverage.

fstats

The output from calculateStats.

regions

The output from calculatePvalues.

annotation

The output from matchGenes.

These are the same components that are written to Rdata files if writeOutput=TRUE.

Author(s)

Leonardo Collado-Torres

See Also

makeModels, preprocessCoverage, calculateStats, calculatePvalues, annotateTranscripts, matchGenes

Examples

## Collapse the coverage information
collapsedFull <- collapseFullCoverage(list(genomeData$coverage),
    verbose = TRUE
)

## Calculate library size adjustments
sampleDepths <- sampleDepth(collapsedFull,
    probs = c(0.5), nonzero = TRUE,
    verbose = TRUE
)

## Build the models
groupInfo <- genomeInfo$pop
adjustvars <- data.frame(genomeInfo$gender)
models <- makeModels(sampleDepths, testvars = groupInfo, adjustvars = adjustvars)

## Analyze the chromosome
results <- analyzeChr(
    chr = "21", coverageInfo = genomeData, models = models,
    cutoffFstat = 1, cutoffType = "manual", groupInfo = groupInfo, mc.cores = 1,
    writeOutput = FALSE, returnOutput = TRUE, method = "regular",
    runAnnotation = FALSE
)
names(results)

lcolladotor/derfinder documentation built on Dec. 17, 2024, 4:53 p.m.