init.filenames: Init file names for analysis

Description Usage Arguments Value Author(s)

View source: R/init.filenames.R

Description

Init the names for the files to use in the analysis to come. Specifically the name of the files with the bin counts and compressed bin counts are created. Normalized bin counts, Z-scores, fold-changes will also be written following the paths created by this function.

Usage

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init.filenames(files.df, dest.folder = ".", sample.folder = TRUE,
  code = NULL, dest.folder.relative.path = TRUE, sub.folder = NULL)

Arguments

files.df

a data.frame with the information about the files to use. Columns 'sample' and 'bam' are required.

dest.folder

the folder where the files with the bin counts are to be created.

sample.folder

if TRUE (default), a folder is created for each sample on the specified destination folder.

code

if not NULL, a name for the analysis. Useful when PopSV is to be run several times with different parameters. Default is NULL.

dest.folder.relative.path

Is the specified folder defined relatively to the working directory. Default is TRUE. Set to FALSE if providing absolute paths (recommended).

sub.folder

if non-null, sample folders will be structure into sub folder defined by the column in 'files.df' named according to 'sub.folder's value. Useful when many samples from different projects are studied together.

Value

an updated data.frame with the information about the files. For example a new column 'bc', 'bc.gz', 'bc.gc' and 'bc.gc.bz' holds the name of the bin counts (raw/compressed), GC corrected bin counts (raw/compressed) files to be created later.

Author(s)

Jean Monlong


jmonlong/PopSV documentation built on Sept. 15, 2019, 9:29 p.m.