downsizeMatrix: downsizeMatrix

In eprifti/momr: Mining Metaomics Data (MetaOMineR)

downsizeMatrix

Description

takes a matrix with raw read gene counts and converts it to a downsized matrix with identical number of mapped reads for each sample (column)

Usage

downsizeMatrix(
  data,
  level = 1.1e+07,
  HQ_reads = NULL,
  repetitions = 1,
  silent = FALSE
)

Arguments

data	: raw read count matrix with gene_ids as rownames
level	: default 11E06, the downsizing levels number of reads to be selected randomly.
HQ_reads	: To take into account a vector of high quality reads that are not mapped.
repetitions	: default 1, This can be also computed several times, but one is the error minimal downsizing strategy
silent	: default is FALSE prints the status of downsizing

Details

downsizeMatrix

Value

downsized read gene count matrix corresponding to the mean counts obtained with the selected number of independant downsizing procedure

Note

if the downsizing level is higher than the number of reads for a given sample than the result will be NA

Author(s)

Edi Prifti & Emmanuelle Le Chatelier

eprifti/momr documentation built on Sept. 27, 2022, 3:36 a.m.