PeakCallingFseq: Use F-seq to call peak

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Use F-seq to call peak

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
atacPeakCalling(
  atacProc,
  bedInput = NULL,
  background = NULL,
  genomicReadsCount = NULL,
  fragmentSize = 0,
  featureLength = NULL,
  bedOutput = NULL,
  ploidyDir = NULL,
  fileformat = c("bed", "wig", "npf"),
  wiggleTrackStep = NULL,
  threshold = NULL,
  verbose = TRUE,
  wgThresholdSet = NULL,
  ...
)

## S4 method for signature 'ATACProc'
atacPeakCalling(
  atacProc,
  bedInput = NULL,
  background = NULL,
  genomicReadsCount = NULL,
  fragmentSize = 0,
  featureLength = NULL,
  bedOutput = NULL,
  ploidyDir = NULL,
  fileformat = c("bed", "wig", "npf"),
  wiggleTrackStep = NULL,
  threshold = NULL,
  verbose = TRUE,
  wgThresholdSet = NULL,
  ...
)

peakCalling(
  bedInput,
  background = NULL,
  genomicReadsCount = NULL,
  fragmentSize = 0,
  featureLength = NULL,
  bedOutput = NULL,
  ploidyDir = NULL,
  fileformat = c("bed", "wig", "npf"),
  wiggleTrackStep = NULL,
  threshold = NULL,
  verbose = TRUE,
  wgThresholdSet = NULL,
  ...
)

Arguments

atacProc

ATACProc-class object scalar. It has to be the return value of upstream process: atacSamToBed, atacBedUtils.

bedInput

Character scalar. BED file input path.

background

Character scalar. background directory default: NULL (none)

genomicReadsCount

Integer scalar. genomic count of sequence reads. default: NULL (calculated)

fragmentSize

Integer scalar. fragment size. set NULL to estimat from data. default:0

featureLength

Character scalar. feature length default: NULL (600)

bedOutput

Character scalar. the output bed file path

ploidyDir

Character scalar. ploidy/input directory. default: NULL

fileformat

Character scalar. File format of result. default: bed

wiggleTrackStep

Integer scalar. wiggle track step default: NULL (1)

threshold

Numeric scalar. threshold (standard deviations) default: NULL (4.0)

verbose

Logical scalar. verbose output if TRUE.

wgThresholdSet

Character scalar. wg threshold set default: NULL (calculated)

...

Additional arguments, currently unused.

Details

The parameter related to input and output file path will be automatically obtained from ATACProc-class object(atacProc) or generated based on known parameters if their values are default(e.g. NULL). Otherwise, the generated values will be overwrited. If you want to use this function independently, you can use peakCalling instead.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Zheng Wei

See Also

atacSamToBed samToBed atacBedUtils bedUtils

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
library(R.utils)
library(magrittr)
td <- tempdir()
setTmpDir(td)

bedbzfile <- system.file(package="esATAC", "extdata", "chr20.50000.bed.bz2")
bedfile <- file.path(td,"chr20.50000.bed")
bunzip2(bedbzfile,destname=bedfile,overwrite=TRUE,remove=FALSE)

bedUtils(bedInput = bedfile,maxFragLen = 100, chrFilterList = NULL) %>%
atacPeakCalling

dir(td)

esATAC documentation built on Nov. 8, 2020, 6:58 p.m.