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()

[Package autonomics version 1.2.0 Index]