export.wiggle: Export as wiggle format

In JokingHero/ORFik: Open Reading Frames in Genomics

Export as wiggle format

Description

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

Usage

export.wiggle(x, file)

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.
file	a character path to valid output file name

Value

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

References

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

See Also

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

Examples

x <- c(GRanges("1", c(1,3,5), "-"), GRanges("1", c(1,3,5), "+"))
# export.wiggle(x, "output/path/rna.wig")

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