convert_to_covRleList: Convert libraries to covRleList objects

In JokingHero/ORFik: Open Reading Frames in Genomics

Convert libraries to covRleList objects

Description

Useful to store reads separated by readlength, for much faster coverage calculation. Saved by default in folder "cov_RLE_List" relative to default libraries of experiment

Usage

convert_to_covRleList(
  df,
  in_files = filepath(df, "pshifted"),
  out_dir = file.path(libFolder(df), "cov_RLE_List"),
  out_dir_merged = file.path(libFolder(df), "cov_RLE"),
  split.by.strand = TRUE,
  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_List").
out_dir_merged	character vector of paths, default: file.path(libFolder(df), "cov_RLE"). Paths to merged output files, Set to NULL to skip making merged covRle.
split.by.strand	logical, default TRUE, split into forward and reverse strand RleList inside covRle object.
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_covRle()

Examples

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

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