CutSiteCountR: Count cut site number in given motif region and plot...

In wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis

Count cut site number in given motif region and plot footprint.

Description

This function is used to count cut site number in given motif regions and plot footprint. Multi-motif is supported. NOTE: The input parameter is a a little bit complex, atacExtractCutSite and atacMotifScan is recommended to use which makes the entire procedure easier.

Usage

atacCutSiteCount(
  atacProcCutSite,
  atacProcMotifScan = NULL,
  csInput = NULL,
  motif_info = NULL,
  chr = c(1:22, "X", "Y"),
  matrixOutput = NULL,
  strandLength = 100,
  FootPrint = TRUE,
  prefix = NULL,
  ...
)

## S4 method for signature 'ATACProc'
atacCutSiteCount(
  atacProcCutSite,
  atacProcMotifScan = NULL,
  csInput = NULL,
  motif_info = NULL,
  chr = c(1:22, "X", "Y"),
  matrixOutput = NULL,
  strandLength = 100,
  FootPrint = TRUE,
  prefix = NULL,
  ...
)

cutsitecount(
  csInput = NULL,
  motif_info = NULL,
  chr = c(1:22, "X", "Y"),
  matrixOutput = NULL,
  strandLength = 100,
  FootPrint = TRUE,
  prefix = NULL,
  ...
)

Arguments

atacProcCutSite	ATACProc-class object scalar. It has to be the return value of upstream process: atacExtractCutSite.
atacProcMotifScan	ATACProc-class object scalar. It has to be the return value of upstream process: atacMotifScan.
csInput	Your cut site information file(from atacExtractCutSite function, separated by chromatin name and all cut site are sorted) path with prefix. e.g. "/your_cut_site_information_path/prefix".
motif_info	A rds file from function atacMotifScan. In the rds file, it saves 3 column information(motif, motif exact position information file path and motif length).
chr	Which chromatin the program will processing. It must be identical with the filename of cut site information files or subset of . Default:c(1:22, "X", "Y").
matrixOutput	The output directory, where to save your cut site count of every motif position. an empty folder would be great. Default:tmpdir/Footprint
strandLength	How many bp(base pair) do you want to count up/downstream of the motif. default:100.
FootPrint	TRUE or FALSE, plot footprint or not.
prefix	prefix for the pdf file.
...	Additional arguments, currently unused.

Details

The parameter is simplified because of too many input file. parameter atacProcCutSite and atacProcMotifScan contains all input information so function atacExtractCutSite and atacMotifScan is recommended to use together. For instance, if you want footprint of 3 TFs (transcription factor) of human in chr1-22, X, Y, then you need 24 chromatin cut site files, 3 motif position files as well as 3 integers of the motif. Function atacExtractCutSite and atacMotifScan will do all this, you just specify which motif you want. Therefore, atacExtractCutSite and atacMotifScan is recommended to use together.

Value

An invisible ATACProc-class object scalar.

Author(s)

Wei Zhang

See Also

atacExtractCutSite atacMotifScan

Examples

library(R.utils)
library(BSgenome.Hsapiens.UCSC.hg19)
## processing bed file
fra_path <- system.file("extdata", "chr20.50000.bed.bz2", package="esATAC")
frag <- as.vector(bunzip2(filename = fra_path,
destname = file.path(getwd(), "chr20.50000.bed"),
ext="bz2", FUN=bzfile, overwrite=TRUE, remove = FALSE))
cs.data <- extractcutsite(bedInput = frag, prefix = "ATAC")

## find motif position
p1bz <- system.file("extdata", "Example_peak1.bed.bz2", package="esATAC")
peak1_path <- as.vector(bunzip2(filename = p1bz,
destname = file.path(getwd(), "Example_peak1.bed"),
ext="bz2", FUN = bzfile, overwrite=TRUE, remove = FALSE))
# motif <- readRDS(system.file("extdata", "MotifPFM.rds", package="esATAC"))
# motif.data <- motifscan(peak = peak1_path, genome = BSgenome.Hsapiens.UCSC.hg19, motifs = motif)

## plot footprint
# atacCutSiteCount(atacProcCutSite = cs.data, atacProcMotifScan = motif.data)

wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.