enrichedFragments {ATACseqQC} | R Documentation

## enrichment for nucleosome-free fragments and nucleosome signals

### Description

Get the enrichment signals for nucleosome-free fagments and nucleosomes.

### Usage

    enrichedFragments(
      bamfiles,
      index = bamfiles,
      gal,
      TSS,
      librarySize,
      upstream = 1010L,
      downstream = 1010L,
      n.tile = 101L,
      normal.method = "quantile",
      adjustFragmentLength = 80L,
      TSS.filter = 0.5,
      seqlev = paste0("chr", c(1:22, "X", "Y"))
    )

### Arguments

`bamfiles` | A vector of characters indicates the file names of bams.
`index` | The names of the index file of the 'BAM' file being processed; This is given without the '.bai' extension.
`gal` | A GAlignmentsList object or a list of GAlignmentPairs. If bamfiles is missing, gal is required.
`TSS` | an object of GRanges indicates the transcript start sites. All the width of TSS should equal to 1. Otherwise, TSS will be reset to the center of input TSS.
`librarySize` | A vector of numeric indicates the library size. Output of estLibSize
`upstream, downstream` | numeric(1) or integer(1). Upstream and downstream size from each TSS.
`n.tile` | numeric(1) or integer(1). The number of tiles to generate for each element of TSS.
`normal.method` | character(1). Normalization methods, could be "none" or "quantile". See normalizeBetweenArrays.
`adjustFragmentLength` | numeric(1) or integer(1). The size of fragment to be adjusted to. Default is set to half of the nucleosome size (80)
`TSS.filter` | numeric(1). The filter for signal strength of each TSS. Default 0.5 indicates the average signal strength for the TSS from upstream to downstream bins should be greater than 0.5.
`seqlev` | A vector of character indicates the sequence names to be considered.

### Value

A list of matrixes. In each matrix, each row record the signals for corresponding feature.

### Author(s)

Jianhong Ou

### Examples

    bamfiles <- system.file("extdata", "splited",
                           c("NucleosomeFree.bam",
                             "mononucleosome.bam",
                             "dinucleosome.bam",
                             "trinucleosome.bam"), package="ATACseqQC")
    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
    txs <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene)
    TSS <- promoters(txs, upstream=0, downstream=1)
    library(ChIPpeakAnno)
    librarySize <- estLibSize(bamfiles)
    sigs <- enrichedFragments(bamfiles, TSS=TSS, librarySize=librarySize,
                              seqlev="chr1", TSS.filter=0)
    sigs.log2 <- lapply(sigs, function(.ele) log2(.ele+1))
    featureAlignedHeatmap(sigs.log2, reCenterPeaks(TSS, width=2020),
                          zeroAt=.5, n.tile=101, upper.extreme=2)
    featureAlignedDistribution(sigs, reCenterPeaks(TSS, width=2020),
                               zeroAt=.5, n.tile=101, type="l")

[Package ATACseqQC version 1.11.8 Index]