initializeResults {regsplice} | R Documentation |
Initialize a RegspliceResults
object, which will contain the results of the
regsplice
analysis.
initializeResults(rs_data)
rs_data |
|
Creates a RegspliceResults
object containing gene names only.
This object will subsequently be populated using the functions
fitRegMultiple
, fitNullMultiple
,
fitFullMultiple
, and LRTests
.
Previous step: Calculate limma-voom
transformation and weights with
runVoom
.
Next step: Fit models with fitRegMultiple
,
fitNullMultiple
, and fitFullMultiple
.
Returns a RegspliceResults
object containing gene IDs
only.
RegspliceData
RegspliceResults
fitRegMultiple
fitNullMultiple
fitFullMultiple
LRTests
summaryTable
file_counts <- system.file("extdata/vignette_counts.txt", package = "regsplice") data <- read.table(file_counts, header = TRUE, sep = "\t", stringsAsFactors = FALSE) head(data) counts <- data[, 2:7] tbl_exons <- table(sapply(strsplit(data$exon, ":"), function(s) s[[1]])) gene_IDs <- names(tbl_exons) n_exons <- unname(tbl_exons) condition <- rep(c("untreated", "treated"), each = 3) rs_data <- RegspliceData(counts, gene_IDs, n_exons, condition) rs_data <- filterZeros(rs_data) rs_data <- filterLowCounts(rs_data) rs_data <- runNormalization(rs_data) rs_data <- runVoom(rs_data) rs_results <- initializeResults(rs_data)