convert_to_covRle: Convert libraries to covRle

In JokingHero/ORFik: Open Reading Frames in Genomics

Convert libraries to covRle

Description

Saved by default in folder "cov_RLE" relative to default libraries of experiment

Usage

convert_to_covRle(
  df,
  in_files = filepath(df, "pshifted"),
  out_dir = file.path(libFolder(df), "cov_RLE"),
  split.by.strand = TRUE,
  split.by.readlength = FALSE,
  seq_info = seqinfo(df),
  weight = "score",
  verbose = TRUE
)

Arguments

df	an ORFik experiment, or NULL is allowed if both in_files and out_dir is specified manually.
in_files	paths to input files, default pshifted files: filepath(df, "pshifted") in ofst format
out_dir	paths to output files, default file.path(libFolder(df), "cov_RLE").
split.by.strand	logical, default TRUE, split into forward and reverse strand RleList inside covRle object.
split.by.readlength	logical, default FALSE, split into files for each readlength, defined by readWidths(x) for each file.
seq_info	SeqInfo object, default seqinfo(findFa(df))
weight	integer, numeric or single length character. Default "score". Use score column in loaded in_files.
verbose	logical, default TRUE, message about library output status.

Value

invisible(NULL), files saved to disc

See Also

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

Examples

df <- ORFik.template.experiment()[10,]
## Usually do default folder, here we use tmpdir
folder_to_save <- file.path(tempdir(), "cov_RLE")
convert_to_covRle(df, out_dir = folder_to_save)
fimport(file.path(folder_to_save, "RFP_Mutant_rep2.covrds"))

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