callpeak | R Documentation |
Main MACS3 Function to call peaks from alignment results.
callpeak(
tfile,
cfile = NULL,
gsize = "hs",
tsize = NULL,
format = "AUTO",
keepduplicates = "1",
outdir = ".",
name = "NA",
store_bdg = FALSE,
do_SPMR = FALSE,
trackline = FALSE,
nomodel = FALSE,
shift = 0,
extsize = 200,
bw = 300,
d_min = 20,
mfold = c(5, 50),
onauto = FALSE,
qvalue = 0.05,
pvalue = NULL,
tempdir = "/tmp",
nolambda = FALSE,
scaleto = "small",
downsample = FALSE,
slocal = 1000,
llocal = 10000,
broad = FALSE,
broadcutoff = 0.1,
maxgap = NULL,
minlen = NULL,
cutoff_analysis = FALSE,
fecutoff = 0.1,
call_summits = FALSE,
buffer_size = 1e+05,
verbose = 2L,
log = TRUE,
...
)
tfile |
ChIP-seq treatment files. |
cfile |
Control files. |
gsize |
Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs. |
tsize |
Tag size/read length. This will override the auto detected tag size. DEFAULT: Not set |
format |
Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or "SAM" or "BAM" or "BOWTIE" or "BAMPE" or "BEDPE". |
keepduplicates |
It controls the behavior towards duplicate tags at the exact same location – the same coordination and the same strand. |
outdir |
If specified all output files will be written to that directory. |
name |
Experiment name, which will be used to generate output file names. |
store_bdg |
Whether or not to save extended fragment pileup, and local lambda tracks (two files) at every bp into a bedGraph file. |
do_SPMR |
If True, MACS will SAVE signal per million reads for fragment pileup profiles. |
trackline |
Tells MACS to include trackline with bedGraph files. |
nomodel |
Whether or not to build the shifting model. |
shift |
The arbitrary shift in bp. Use discretion while setting it other than default value. |
extsize |
The arbitrary extension size in bp. |
bw |
Band width for picking regions to compute fragment size. |
d_min |
Minimum fragment size in basepair. Any predicted fragment size less than this will be excluded. |
mfold |
Select the regions within MFOLD range of high-confidence enrichment ratio against background to build model. |
onauto |
Whether turn on the auto pair model process. |
qvalue |
Minimum FDR (q-value) cutoff for peak detection. |
pvalue |
Pvalue cutoff for peak detection. DEFAULT: not set. |
tempdir |
Optional directory to store temp files. |
nolambda |
If True, MACS will use fixed background lambda as local lambda for every peak region. |
scaleto |
When set to 'small', scale the larger sample up to the smaller sample. |
downsample |
When set, random sampling method will scale down the bigger sample. By default, MACS uses linear scaling. |
slocal |
The small nearby region in basepairs to calculate dynamic lambda. |
llocal |
The large nearby region in basepairs to calculate dynamic lambda. |
broad |
If set, MACS will try to call broad peaks using the –broad-cutoff setting. |
broadcutoff |
Cutoff for broad region. This option is not available unless –broad is set. |
maxgap |
Maximum gap between significant sites to cluster them together. The DEFAULT value is the detected read length/tag size. |
minlen |
Minimum length of a peak. The DEFAULT value is the predicted fragment size d. |
cutoff_analysis |
While set, MACS2 will analyze number or total length of peaks that can be called by different p-value cutoff then output a summary table to help user decide a better cutoff. |
fecutoff |
When set, the value will be used to filter out peaks with low fold-enrichment. |
call_summits |
If set, MACS will use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region. |
buffer_size |
Buffer size for incrementally increasing internal array size to store reads alignment information. DEFAULT: 100000. |
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 |
log |
Whether to capture logs. |
... |
More options for macs2. |
macsList
object.
eh <- ExperimentHub::ExperimentHub()
CHIP <- eh[["EH4558"]]
CTRL <- eh[["EH4563"]]
res <- callpeak(CHIP, CTRL, gsize = 5.2e7,
cutoff_analysis = TRUE,
outdir = tempdir(),
name = "callpeak_narrow0")
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