validateCountsCollection: Check a counts collection
In ctlab/phantasus: Visual and interactive gene expression analysis

validateCountsCollection

R Documentation

Check a counts collection

Description

Function checks existing and structure of meta.txt file in specified counts folder.Also it checks accessibility of specified datasets in corresponding .h5 files.

Usage

validateCountsCollection(collectionDir, verbose = FALSE)

Arguments

`collectionDir`	path to directory with collection
`verbose`	logical value which determines a content of the output.

Details

collectionDir should contain a bunch of .h5 files and a single meta.txt. meta.txt is .tsv-like file where for each .h5 exists a row wit columns:

file_name: name of .h5 file in collectionDir.
sample_id: name of dataset in file_name which contains sample IDs (sample_geo_accession for example).
sample_dim: which dimension of the expression matrix in file_name corresponds to samples. Should be one of c("rows", "columns")
gene_id: name of dataset in file_name which contains ids for genes and the "meaning" for that ids( column name in result ES). For correct work this dataset should contain unique values. Example: ENSEMBLID:/meta/genes/ensembl_gene_id
genes_annot: Names of datasets and their meanings to extract gene-related metadata from file_name. Can be empty or gene_id-like values separated with semicolon(;).