bdgdiff: bdgdiff

In macs3-project/MACSr: MACS: Model-based Analysis for ChIP-Seq

bdgdiff

Description

Differential peak detection based on paired four bedgraph files. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS3 are accpetable.

Usage

bdgdiff(
  t1bdg,
  t2bdg,
  c1bdg,
  c2bdg,
  cutoff = 3,
  minlen = 200L,
  maxgap = 100L,
  depth1 = 1,
  depth2 = 1,
  outdir = ".",
  oprefix = character(),
  outputfile = list(),
  log = TRUE,
  verbose = 2L
)

Arguments

t1bdg	MACS pileup bedGraph for condition 1. Incompatible with callpeak –SPMR output. REQUIRED
t2bdg	MACS pileup bedGraph for condition 2. Incompatible with callpeak –SPMR output. REQUIRED
c1bdg	MACS control lambda bedGraph for condition 1. Incompatible with callpeak –SPMR output. REQUIRED
c2bdg	MACS control lambda bedGraph for condition 2. Incompatible with callpeak –SPMR output. REQUIRED
cutoff	logLR cutoff. DEFAULT: 3 (likelihood ratio=1000)", default = 3
minlen	Minimum length of differential region. Try bigger value to remove small regions. DEFAULT: 200", default = 200
maxgap	Maximum gap to merge nearby differential regions. Consider a wider gap for broad marks. Maximum gap should be smaller than minimum length (-g). DEFAULT: 100", default = 100
depth1	Sequencing depth (# of non-redundant reads in million) for condition 1. It will be used together with –d2. See description for –d2 below for how to assign them. Default: 1
depth2	Sequencing depth (# of non-redundant reads in million) for condition 2. It will be used together with –d1. DEPTH1 and DEPTH2 will be used to calculate scaling factor for each sample, to down-scale larger sample to the level of smaller one. For example, while comparing 10 million condition 1 and 20 million condition 2, use –d1 10 –d2 20, then pileup value in bedGraph for condition 2 will be divided by 2. Default: 1
outdir	The output directory.
oprefix	Output file prefix. Actual files will be named as PREFIX_cond1.bed, PREFIX_cond2.bed and PREFIX_common.bed. Mutually exclusive with -o/–ofile.
outputfile	Output filenames. Must give three arguments in order: 1. file for unique regions in condition 1; 2. file for unique regions in condition 2; 3. file for common regions in both conditions. Note: mutually exclusive with –o-prefix.
log	Whether to capture logs.
verbose	Set verbose level of runtime message. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. DEFAULT:2

Value

macsList object.

Examples

eh <- ExperimentHub::ExperimentHub()
CHIP <- eh[["EH4558"]]
CTRL <- eh[["EH4563"]]
c1 <- callpeak(CHIP, CTRL, gsize = 5.2e7, cutoff_analysis = TRUE,
               outdir = tempdir(), name = "callpeak_narrow0", store_bdg = TRUE)
c2 <- callpeak(CHIP, CTRL, gsize = 1e7, nomodel = TRUE, extsize = 250,
               outdir = tempdir(), name = "callpeak_narrow_revert", store_bdg = TRUE)
t1bdg <- grep("treat_pileup", c1$outputs, value = TRUE)
c1bdg <- grep("control_lambda", c1$outputs, value = TRUE)
t2bdg <- grep("treat_pileup", c2$outputs, value = TRUE)
c2bdg <- grep("control_lambda", c2$outputs, value = TRUE)
bdgdiff(t1bdg, t2bdg, c1bdg, c2bdg,
        outdir = tempdir(), oprefix = "bdgdiff")

macs3-project/MACSr documentation built on Nov. 24, 2023, 12:47 p.m.