.read_rnaseq_bams {autonomics}R Documentation

Read rnaseq

Description

Read/analyze rnaseq counts / bamfiles

Usage

.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
)

Arguments

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

Value

SummarizedExperiment

Author(s)

Aditya Bhagwat, Shahina Hayat

Examples

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)

[Package autonomics version 1.1.7 Index]