enrichedFragments: enrichment for nucleosome-free fragments and nucleosome...

In jianhong/ATACseqQC: ATAC-seq Quality Control

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")

jianhong/ATACseqQC documentation built on March 19, 2024, 8:30 a.m.