simpleLibs: Converted format of NGS libraries

In JokingHero/ORFik: Open Reading Frames in Genomics

Converted format of NGS libraries

Description

Export as either .ofst, .wig, .bigWig,.bedo (legacy format) or .bedoc (legacy format) files:
Export files as .ofst for fastest load speed into R.
Export files as .wig / bigWig for use in IGV or other genome browsers.
The input files are checked if they exist from: envExp(df).

Usage

simpleLibs(
  df,
  out.dir = libFolder(df),
  addScoreColumn = TRUE,
  addSizeColumn = TRUE,
  must.overlap = NULL,
  method = "None",
  type = "ofst",
  input.type = "ofst",
  reassign.when.saving = FALSE,
  envir = envExp(df),
  force = TRUE,
  library.names = bamVarName(df),
  libs = outputLibs(df, type = input.type, chrStyle = must.overlap, library.names =
    library.names, output.mode = "list", force = force, BPPARAM = BPPARAM),
  BPPARAM = bpparam()
)

Arguments

df	an ORFik experiment
out.dir	optional output directory, default: libFolder(df), if it is NULL, it will just reassign R objects to simplified libraries. Will then create a final folder specfied as: paste0(out.dir, "/", type, "/"). Here the files will be saved in format given by the type argument.
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 (GAlignment version of.ofst) or .bedoc. Since they contain the original cigar.
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	character, output format, default "ofst". Alternatives: "ofst", "bigWig", "wig","bedo" or "bedoc". Which format you want. Will make a folder within out.dir with this name containing the files.
input.type	character, input type "ofst". Remember this function uses the loaded libraries if existing, so this argument is usually ignored. Only used if files do not already exist.
reassign.when.saving	logical, default FALSE. If TRUE, will reassign library to converted form after saving. Ignored when out.dir = NULL.
envir	environment to save to, default envExp(df), which defaults to .GlobalEnv, but can be set with envExp(df) <- new.env() etc.
force	logical, default TRUE If TRUE, reload library files even if matching named variables are found in environment used by experiment (see envExp) A simple way to make sure correct libraries are always loaded. FALSE is faster if data is loaded correctly already.
library.names	character vector, names of libraries, default: name_decider(df, naming)
libs	list, output of outputLibs as list of GRanges/GAlignments/GAlignmentPairs objects. Set input.type and force arguments to define parameters.
BPPARAM	how many cores/threads to use? default: bpparam(). To see number of threads used, do bpparam()$workers. You can also add a time remaining bar, for a more detailed pipeline.

Details

We advice you to not use this directly, as other function are more safe for library type conversions. See family description below. This is mostly used internally in ORFik. It is only adviced to use if large bam files are already loaded in R and conversions are wanted from those.

See export.ofst, export.wiggle, export.bedo and export.bedoc for information on file formats.
If libraries of the experiment are already loaded into environment (default: .globalEnv) is will export using those files as templates. If they are not in environment the .ofst files from the bam files are loaded (unless you are converting to .ofst then the .bam files are loaded).

Value

invisible NULL (saves files to disc or R .GlobalEnv)

See Also

Other lib_converters: convert_bam_to_ofst(), convert_to_bigWig(), convert_to_covRle(), convert_to_covRleList()

Examples

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

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