downsizeGC.all

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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

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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

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