View source: R/analyzeDuprates.R
analyzeDuprates | R Documentation |
analyzeDuprates
returns a data.frame with tag counts
analyzeDuprates(
bam,
gtf,
stranded = 0,
paired = FALSE,
threads = 1,
verbose = FALSE,
...
)
bam |
The bam file containing the duplicate-marked reads |
gtf |
The gtf file describing the features |
stranded |
Whether the reads are strand specific |
paired |
Paired end experiment? |
threads |
The number of threads to be used for counting |
verbose |
Whether to output Rsubread messages into the console |
... |
Other params sent to featureCounts |
This function makes use of the Rsubread package to count tags on the GTF features in different scenarios. The scenarios are the 4 possible combinations of allowing multimappers (yes/no) and duplicate reads (yes/no).
A data.frame with counts on features, with and without taking into account multimappers/duplicated reads
bam <- system.file("extdata",
"wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2_duprm.bam",
package="dupRadar")
gtf <- system.file("extdata","genes.gtf",package="dupRadar")
stranded <- 2 # '0' (unstranded), '1' (stranded) and '2' (reverse)
paired <- FALSE
threads <- 4
# call the duplicate marker and analyze the reads
dm <- analyzeDuprates(bam,gtf,stranded,paired,threads)
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