preprocess_rnaseq_counts {autonomics}

R Documentation

Preprocess RNAseq counts

Description

Preprocess RNAseq counts

Usage

preprocess_rnaseq_counts(
  object,
  subgroupvar = if ("subgroup" %in% svars(object)) "subgroup" else NULL,
  formula = default_formula(object, subgroupvar, "limma"),
  block = NULL,
  min_count = 10,
  pseudocount = 0.5,
  genesize = NULL,
  cpm = TRUE,
  tmm = cpm,
  voom = TRUE,
  log2 = TRUE,
  verbose = TRUE,
  plot = TRUE
)

Arguments

object	SummarizedExperiment
subgroupvar	subgroup svar
formula	designmat formula
block	blocK svar
min_count	min count required in some samples
pseudocount	added pseudocount to avoid log(x)=-Inf
genesize	genesize fvar to compute tpm
cpm	whether to compute counts per million (scaled) reads
tmm	whether to tmm normalize
voom	whether to voom weight
log2	whether to log2
verbose	whether to msg
plot	whether to plot

Value

SummarizedExperiment

Examples

require(magrittr)
file <- download_data('billing19.rnacounts.txt')
object <- .read_rnaseq_counts(file)
object$subgroup
object %<>% preprocess_rnaseq_counts()

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