Description Usage Arguments Details Value See Also Examples
Filter exons with zero RNA-seq read counts in all biological samples.
1 | filterZeros(rs_data)
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rs_data |
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Removes exon bins with zero RNA-seq read counts in all biological samples. Any remaining single-exon genes (after filtering) are also removed (since differential splicing requires multiple exon bins).
Input data is assumed to be in the form of a RegspliceData
object. See
RegspliceData
for details.
After filtering zero-count exon bins, any remaining genes containing only a single exon bin are also removed (since differential splicing requires multiple exon bins).
Filtering should be skipped when using exon microarray data. (When using the
regsplice
wrapper function, filtering can be disabled with the argument
filter = FALSE
).
Previous step: Create RegspliceData
object with RegspliceData
constructor function.
Next step: Filter low-count exon bins with filterLowCounts
.
Returns a RegspliceData
object.
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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)
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