preprocess_rnaseq_counts: Preprocess RNAseq counts

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

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/autonomics documentation built on Dec. 1, 2024, 12:27 a.m.