parseBamFiles: Function to parse bam files
In umiAnalyzer: Tools for Analyzing Sequencing Data with Unique Molecular Identifiers
Description
Usage
Arguments
Value
Examples
Description
Function to parse bam files
Usage
1
parseBamFiles(mainDir, sampleNames = NULL, consDepth = 0, as.shiny = FALSE)
Arguments
mainDir
Directory containing UMIErrorCorrect output folders.
sampleNames
A list of sample names.
consDepth
Only retain consensus reads of at least cons.depth. Default is 0.
as.shiny
Set to TRUE if run within a shiny::withProgress environment
Value
A data table
Examples
1
2
3
4
5
library(umiAnalyzer)
main <- system.file("extdata", package = "umiAnalyzer")
simsen <- createUmiExperiment(main)
reads <- parseBamFiles(main, consDepth = 10)
umiAnalyzer documentation built on Nov. 25, 2021, 9:07 a.m.
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Description Usage Arguments Value Examples
Description
Function to parse bam files
Usage
1 | parseBamFiles(mainDir, sampleNames = NULL, consDepth = 0, as.shiny = FALSE)
|
Arguments
mainDir |
Directory containing UMIErrorCorrect output folders. |
sampleNames |
A list of sample names. |
consDepth |
Only retain consensus reads of at least cons.depth. Default is 0. |
as.shiny |
Set to TRUE if run within a shiny::withProgress environment |
Value
A data table
Examples
1 2 3 4 5 | library(umiAnalyzer)
main <- system.file("extdata", package = "umiAnalyzer")
simsen <- createUmiExperiment(main)
reads <- parseBamFiles(main, consDepth = 10)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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