pulseTD (version 0.1.0)

estimateExpression: Estimated Expression

Description

This function is used to calculate the expression value of the gene. It includs total exon expression values, total intron expression values, labeled exon expression values, and labeled intron expression values.

Usage

estimateExpression(txdb, filelist, by = "gene", mode = "Union",
  singleEnd = TRUE, ignore.strand = TRUE, fragments = FALSE, ...)

Arguments

txdb

Genomic annotation file

filelist

A vector of sam file paths containing 4sU labeled sam files and unlabeled files

by

In terms of genes or transcripts, the default is the gene

mode

mode can be one of the pre-defined count methods such as "Union", "IntersectionStrict", or "IntersectionNotEmpty" or it a user supplied count function.

singleEnd

(Default TRUE) A logical indicating if reads are single or paired-end.

ignore.strand

A logical indicating if strand should be considered when matching

fragments

(Default FALSE) A logical; applied to paired-end data only. fragments control which function is used to read the data which subsequently affects which records are included in counting.

...

The parameters of the summarizeOverlaps method

Value

A list of expression

See Also

Other parameters summarizeOverlaps

Examples

# NOT RUN {
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
test_path <- file.path(system.file(package="pulseTD"),'extdata/test1.sorted.bam')
test_path2 <- file.path(system.file(package="pulseTD"),'extdata/test2.sorted.bam')
# }
# NOT RUN {
rpkmres <- estimateExpression(txdb,c(test_path,test_path2), by='gene')
# }
# NOT RUN {
data('rpkmres', package='pulseTD')
head(rpkmres$total_exp)
head(rpkmres$pre_exp)
# }