convertLibs: Converted format of NGS libraries

In ORFik: Open Reading Frames in Genomics

Description

Export as either .ofst, .bedo or .bedoc files.
Export files as .bedo files: It is a bed file with 2 score columns. Gives a massive speedup when cigar string and bam flags are not needed.
Export files as .bedoc files: If cigar is needed, gives you replicates and cigar, so a fast way to load a GAlignment object, other bam flags are lost. If type is bedoc addSizeColumn and method will be ignored.

Usage

convertLibs(
  df,
  out.dir = dirname(df$filepath[1]),
  addScoreColumn = TRUE,
  addSizeColumn = TRUE,
  must.overlap = NULL,
  method = "None",
  type = "ofst",
  reassign.when.saving = FALSE,
  envir = .GlobalEnv
)

Arguments

df	an ORFik experiment
out.dir	optional output directory, default: dirname(df$filepath[1]), if it is NULL, it will just reassign R objects to simplified libraries.
addScoreColumn	logical, default TRUE, if FALSE will not add replicate numbers as score column, see ORFik::convertToOneBasedRanges.
addSizeColumn	logical, default TRUE, if FALSE will not add size (width) as size column, see ORFik::convertToOneBasedRanges. Does not apply for .ofst or .bedoc.
must.overlap	default (NULL), else a GRanges / GRangesList object, so only reads that overlap (must.overlap) are kept. This is useful when you only need the reads over transcript annotation or subset etc.
method	character, default "None", the method to reduce ranges, for more info see convertToOneBasedRanges
type	a character of format, default "ofst". Alternatives: "ofst", "wig","bedo" or "bedoc". Which format you want. Will make a folder within out.dir with this name containing the files.
reassign.when.saving	logical, default FALSE. If TRUE, will reassign library to converted form after saving. Ignored when out.dir = NULL.
envir	which environment to save to, default .GlobalEnv

Details

See export.bedo and export.bedoc for information on file formats

Value

NULL (saves files to disc or R .GlobalEnv)

Examples

df <- ORFik.template.experiment()
#convertLibs(df)
# Keep only 5' ends of reads
#convertLibs(df, method = "5prime")

ORFik documentation built on March 27, 2021, 6 p.m.