.read_rnaseq_bams {autonomics} | R Documentation |
Read/analyze rnaseq counts / bamfiles
.read_rnaseq_bams( dir, paired, genome, nthreads = detectCores(), sfile = NULL, sfileby = NULL, subgroupvar = NULL, ffile = NULL, ffileby = NULL, fnamevar = NULL, verbose = TRUE ) .read_rnaseq_counts( file, fid_col = 1, sfile = NULL, sfileby = NULL, ffile = NULL, ffileby = NULL, subgroupvar = NULL, verbose = TRUE ) read_rnaseq_bams( dir, paired, genome, nthreads = detectCores(), sfile = NULL, sfileby = NULL, subgroupvar = NULL, block = NULL, ffile = NULL, ffileby = NULL, fnamevar = NULL, formula = NULL, min_count = 10, pseudocount = 0.5, genesize = NULL, cpm = TRUE, tmm = cpm, log2 = TRUE, pca = FALSE, fit = NULL, voom = !is.null(fit), contrastdefs = NULL, verbose = TRUE, plot = TRUE ) read_rnaseq_counts( file, fid_col = 1, sfile = NULL, sfileby = NULL, subgroupvar = NULL, block = NULL, ffile = NULL, ffileby = NULL, fnamevar = NULL, formula = NULL, min_count = 10, pseudocount = 0.5, genesize = NULL, cpm = TRUE, tmm = cpm, log2 = TRUE, pca = FALSE, fit = NULL, voom = !is.null(fit), contrastdefs = NULL, verbose = TRUE, plot = TRUE )
dir |
read_rnaseq_bams: bam/samfile dir |
paired |
read_rnaseq_bams: whether paired end reads |
genome |
read_rnaseq_bams: mm10"/"hg38"/etc. or GTF file |
nthreads |
read_rnaseq_bams: nthreads used by Rsubread::featureCounts() |
sfile |
sample file |
sfileby |
sample file mergeby column |
subgroupvar |
subgroup svar |
ffile |
feature file |
ffileby |
feature file mergeby column |
fnamevar |
featurename fvar |
verbose |
whether to message |
file |
read_rnaseq_counts: count file |
fid_col |
featureid fvar |
block |
block svar |
formula |
designmat formula |
min_count |
min feature count required in some samples |
pseudocount |
added pseudocount to prevent -Inf log2 values |
genesize |
genesize fvar for tpm |
cpm |
whether to compute cpm |
tmm |
whether to tmm-scale library sizes |
log2 |
whether to log2 transform |
pca |
whether to pca |
fit |
fit model: NULL, 'limma', 'lm', 'lme', 'lmer', 'wilcoxon' |
voom |
whether to compute voom precision weights |
contrastdefs |
contrastdef vector/matrix/list |
plot |
whether to plot |
SummarizedExperiment
Aditya Bhagwat, Shahina Hayat
file <- download_data('billing19.rnacounts.txt') object <- read_rnaseq_counts(file, pca= TRUE, fit='limma') # requires Rsubread # file <- download_data('billing16.bam.zip') # object <- read_rnaseq_bams(file, paired=TRUE, genome='hg38', pca=TRUE, # fit='limma', plot=TRUE)