preprocess_rnaseq_counts: Preprocess RNAseq counts

preprocess_rnaseq_countsR Documentation

Preprocess RNAseq counts

Description

Preprocess RNAseq counts

Usage

preprocess_rnaseq_counts(
  object,
  formula = ~subgroup,
  block = NULL,
  min_count = 10,
  pseudo = 0.5,
  tpm = FALSE,
  cpm = TRUE,
  voom = TRUE,
  log2 = TRUE,
  verbose = TRUE,
  plot = TRUE
)

Arguments

object

SummarizedExperiment

formula

designmat formula

block

blocK svar

min_count

min count required in some samples

pseudo

added pseudocount to avoid log(x)=-Inf

tpm

TRUE or FALSE : tpm normalize?

cpm

TRUE or FALSE : cpm normalize? (counts per million (scaled) reads)

voom

TRUE or FALSE : voom weight?

log2

TRUE or FALSE : log2 transform?

verbose

TRUE or FALSE : msg?

plot

TRUE or FALSE : plot?

Value

SummarizedExperiment

Examples

file <- system.file('extdata/billing19.rnacounts.txt', package = 'autonomics')
object <- .read_rnaseq_counts(file)
object$subgroup
object %<>% preprocess_rnaseq_counts()

bhagwataditya/importomics documentation built on July 11, 2024, 11:26 a.m.