export.bigWig: Export as bigWig format

In JokingHero/ORFik: Open Reading Frames in Genomics

Export as bigWig format

Description

Will create 2 files, 1 for + strand (*_forward.bigWig) and 1 for - strand (*_reverse.bigWig). If all ranges are * stranded, will output 1 file. Can be direct input for ucsc browser or IGV

Usage

export.bigWig(
  x,
  file,
  split.by.strand = TRUE,
  is_pre_collapsed = FALSE,
  seq_info = seqinfo(x)
)

Arguments

x	A GRangesList, GAlignment GAlignmentPairs with score column. Will be converted to 5' end position of original range. If score column does not exist, will group ranges and give replicates as score column. Since bigWig needs a score column to represent counts!
file	a character path to valid output file name
split.by.strand	logical, default TRUE. Split bigWig into 2 files, one for each strand.
is_pre_collapsed	logical, default FALSE. Have you already collapsed reads with collapse.by.scores, so each positions is only in 1 GRanges object with a score column per readlength? Set to TRUE, only if you are sure, will give a speedup.
seq_info	a Seqinfo object, default seqinfo(x). Must have non NA seqlengths defined!

Value

invisible(NULL) (File is saved as 2 .bigWig files)

References

https://genome.ucsc.edu/goldenPath/help/bigWig.html

See Also

Other utils: bedToGR(), convertToOneBasedRanges(), export.bed12(), export.fstwig(), export.wiggle(), fimport(), findFa(), fread.bed(), optimizeReads(), readBam(), readBigWig(), readWig()

Examples

x <- c(GRanges("1", c(1,3,5), "-"), GRanges("1", c(1,3,5), "+"))
seqlengths(x) <- 10
file <- file.path(tempdir(), "rna.bigWig")
# export.bigWig(x, file)
# export.bigWig(covRleFromGR(x), file)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.