bdgpeakcall | R Documentation |
Call peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS3 are accpetable.
bdgpeakcall(
ifile,
cutoff = 5,
minlen = 200L,
maxgap = 30L,
call_summits = FALSE,
cutoff_analysis = FALSE,
trackline = TRUE,
outdir = ".",
outputfile = character(),
log = TRUE,
verbose = 2L
)
ifile |
MACS score in bedGraph. REQUIRED. |
cutoff |
Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS3, score 5 means pvalue 1e-5. DEFAULT: 5", default = 5. |
minlen |
minimum length of peak, better to set it as d value. DEFAULT: 200", default = 200. |
maxgap |
maximum gap between significant points in a peak, better to set it as tag size. DEFAULT: 30", default = 30. |
call_summits |
If set, MACS will use a more sophisticated approach to find all summits in each enriched peak region DEFAULT: False",default=False. |
cutoff_analysis |
While set, bdgpeakcall will analyze number or total length of peaks that can be called by different cutoff then output a summary table to help user decide a better cutoff. Note, minlen and maxgap may affect the results. DEFAULT: False", default = False. |
trackline |
Tells MACS not to include trackline with bedGraph files. The trackline is required by UCSC. |
outdir |
The output directory. |
outputfile |
The output file. |
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 |
macsList
object.
eh <- ExperimentHub::ExperimentHub()
CHIP <- eh[["EH4558"]]
CTRL <- eh[["EH4563"]]
p1 <- pileup(CHIP, outdir = tempdir(),
outputfile = "pileup_ChIP_bed.bdg", format = "BED")
p2 <- pileup(CTRL, outdir = tempdir(),
outputfile = "pileup_CTRL_bed.bdg", format = "BED")
c1 <- bdgcmp(p1$outputs, p2$outputs, outdir = tempdir(),
oprefix = "bdgcmp", pseudocount = 1, method = "FE")
bdgpeakcall(c1$outputs, cutoff = 2,
outdir = tempdir(), outputfile = "bdgpeakcall")
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