pileup

Pileup aligned reads with a given extension size (fragment size or d in MACS language). Note there will be no step for duplicate reads filtering or sequencing depth scaling, so you may need to do certain pre/post-processing.

pileup(
  ifile,
  outputfile = character(),
  outdir = ".",
  format = c("AUTO", "BAM", "SAM", "BED", "ELAND", "ELANDMULTI", "ELANDEXPORT", "BOWTIE",
    "BAMPE", "BEDPE"),
  bothdirection = FALSE,
  extsize = 200L,
  buffer_size = 100000L,
  verbose = 2L,
  log = TRUE
)

Arguments

ifile

Alignment file. If multiple files are given as '-t A B C', then they will all be read and combined. REQUIRED.

outputfile

Output bedGraph file name. If not specified, will write to standard output. REQUIRED.

outdir

The output directory.

format

Format of tag file, \"AUTO\", \"BED\", \"ELAND\", \"ELANDMULTI\", \"ELANDEXPORT\", \"SAM\", \"BAM\", \"BOWTIE\", \"BAMPE\", or \"BEDPE\". The default AUTO option will let '%(prog)s' decide which format the file is. DEFAULT: \"AUTO\", MACS3 will pick a format from \"AUTO\", \"BED\", \"ELAND\", \"ELANDMULTI\", \"ELANDEXPORT\", \"SAM\", \"BAM\" and \"BOWTIE\". If the format is BAMPE or BEDPE, please specify it explicitly. Please note that when the format is BAMPE or BEDPE, the -B and –extsize options would be ignored.

bothdirection

By default, any read will be extended towards downstream direction by extension size. So it's 0,size-1 (1-based index system) for plus strand read and -size+1,0 for minus strand read where position 0 is 5' end of the aligned read. Default behavior can simulate MACS3 way of piling up ChIP sample reads where extension size is set as fragment size/d. If this option is set as on, aligned reads will be extended in both upstream and downstream directions by extension size. It means -size,size where 0 is the 5' end of a aligned read. It can partially simulate MACS3 way of piling up control reads. However MACS3 local bias is calculated by maximizing the expected pileup over a ChIP fragment size/d estimated from 10kb, 1kb, d and whole genome background. This option will be ignored when the format is set as BAMPE or BEDPE. DEFAULT: False

extsize

The extension size in bps. Each alignment read will become a EXTSIZE of fragment, then be piled up. Check description for -B for detail. It's twice the shiftsize in old MACSv1 language. This option will be ignored when the format is set as BAMPE or BEDPE. DEFAULT: 200

buffer_size

Buffer size for incrementally increasing internal array size to store reads alignment information. In most cases, you don't have to change this parameter. However, if there are large number of chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size in order to decrease memory usage (but it will take longer time to read alignment files). Minimum memory requested for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8 Bytes. DEFAULT: 100000

verbose

Set verbose level. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. If you want to know where are the duplicate reads, use 3. DEFAULT:2

log

Whether to capture logs.

Value

macsList object.

Examples

eh <- ExperimentHub::ExperimentHub()
CHIP <- eh[["EH4558"]]
#> see ?MACSdata and browseVignettes('MACSdata') for documentation
#> loading from cache
p <- pileup(CHIP, outdir = tempdir(), outputfile = "pileup_bed.bdg", format = "BED")
#>