export.fstwig: Export as fstwig (fastwig) format

In JokingHero/ORFik: Open Reading Frames in Genomics

Export as fstwig (fastwig) format

Description

Will create 2 files, 1 for + strand (*_forward.fstwig) and 1 for - strand (*_reverse.fstwig). If all ranges are * stranded, will output 1 file.

Usage

export.fstwig(
  x,
  file,
  by.readlength = TRUE,
  by.chromosome = TRUE,
  compress = 50
)

Arguments

x	A GRangesList, GAlignment GAlignmentPairs with score column or coverage RLElist 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
by.readlength	logical, default TRUE
by.chromosome	logical, default TRUE
compress	value in the range 0 to 100, indicating the amount of compression to use. Lower values mean larger file sizes. The default compression is set to 50.

Value

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

References

"TODO"

See Also

Other utils: bedToGR(), convertToOneBasedRanges(), export.bed12(), export.bigWig(), 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), "+"))
x$size <- rep(c(28, 29), length.out = length(x))
x$score <- c(5,1,2,5,1,6)
seqlengths(x) <- 5
# export.fstwig(x, "~/Desktop/ribo")

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