downsizeGC.all: downsizeGC.all

In eprifti/momr: Mining Metaomics Data (MetaOMineR)

downsizeGC.all

Description

This function takes a matrix with raw reads counts and computes the number of genes at different downsizing levels a given number of times. This is similar to the downsizeGC function but for optimization purposes it downsizes at different thresholds all together

Usage

downsizeGC.all(
  data,
  levels = c(seq(1e+06, 1.1e+07, 1e+06)),
  repetitions = 10,
  silent = FALSE
)

Arguments

data	: raw read count matrix with gene_ids as rownames
levels	: default seq(1E06,11E06,1E06), the downsizing levels number of reads to be selected randomly.
repetitions	: default 10, the number of times the drawing is performed. Usually 30 or 10 to speed things out
silent	: default is FALSE prints the status of downsizing

Details

downsizeGC.all

Value

a list of matrixes one per sample containing in rows a vector for each repetition and in columns the number of downsized genes for each downsizing level

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 Dec. 11, 2024, 3:06 p.m.