updateCountsMeta: Update meta-data for counts collections

In ctlab/phantasus: Visual and interactive gene expression analysis

Update meta-data for counts collections

Description

Creates meta.rda file which contain information about all samples in all collections. Also function checks priority.txt file. This file is used to manage collections with the same samples.

Usage

updateCountsMeta(
  counts_dir = getPhantasusConf("cache_folders")$rnaseq_counts,
  force = FALSE,
  verbose = FALSE
)

Arguments

counts_dir	path to counts cache directory
force	logical value wich lets function replace existing meta.rda file
verbose	logical value which determines a content of the output.

Details

First of all function checks validity of priority.txt file. Every Collection should have unique priority. If priority.txt is not valid function creates new one, setting priorities for each subdirectory(=collection) equal to order in list.dir output.

Function updates meta.rda if this file is older than at least one .h5 file in counts files. meta.rda is data.table which is a result of union data.tables produced by getCountsMetaPart for each collection

See Also

validateCountsCollection,updateCountsMeta

ctlab/phantasus documentation built on Oct. 11, 2024, 4:11 p.m.