pooled_peaks_macsr: Call consensus peaks: 'MACSr'

In neurogenomics/PeakyFinders: Mining, Calling, and Importing Epigenomic Peaks in R

Call consensus peaks: MACSr

Description

Call consensus peaks by merging groups of BAM files with mergeBam and then calling peaks with callpeak.

Usage

pooled_peaks_macsr(
  bam_files,
  outdir = tempdir(),
  g = NULL,
  overwrite = TRUE,
  verbose = TRUE,
  ...
)

Arguments

bam_files	One or more BAM files.
outdir	Directory to save results to.
overwrite	A logical(1) indicating whether the destination can be over-written if it already exists.
verbose	Print messages.
...	Arguments passed on to MACSr::callpeak 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. 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. log Whether to capture logs.

Value

GRanges object.

neurogenomics/PeakyFinders documentation built on March 24, 2024, 4:28 p.m.