preprocess_rnaseq_counts {autonomics} | R Documentation |
Preprocess RNAseq counts
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 )
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 |
SummarizedExperiment
require(magrittr) file <- download_data('billing19.rnacounts.txt') object <- .read_rnaseq_counts(file) object$subgroup object %<>% preprocess_rnaseq_counts()