SummarizeUniqueReads: Get a summary of the unique reads from bam file. Duplicate...
In njmadrid/RNAseqQuality: Provides a set of functions for summarizing the quality of RNA-seq data.
Description
Usage
Arguments
Value
Author(s)
Examples
Description
unique aligned reads = total number of reads that are not secondary;
uniquely aligned reads without duplicates = total number of reads that are not secondary and not duplicates;
duplicate reads = total number of reads that are duplicates;
Usage
1
SummarizeUniqueReads(BamFilePath)
Arguments
BamFilePath
location of aligned bam file. Corresponding bai index file must be in the same directory.
Value
A data.frame containing a summary of the unique reads from bam file. Duplicate reads are defined as having identical pos and cigar values.
Author(s)
Nathaniel J. Madrid, Jason Byars
Examples
1
2
BamFilePaths <- dir(path="/home/ubuntu/Projects/RNAseqPackage/bams", pattern=".*.bam$", full.names=T)
UniqueReadsDF = SummarizeUniqueReads(BamFilePaths[1])
njmadrid/RNAseqQuality documentation built on May 20, 2019, 3:32 p.m.
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Description Usage Arguments Value Author(s) Examples
Description
unique aligned reads = total number of reads that are not secondary; uniquely aligned reads without duplicates = total number of reads that are not secondary and not duplicates; duplicate reads = total number of reads that are duplicates;
Usage
1 | SummarizeUniqueReads(BamFilePath)
|
Arguments
BamFilePath |
location of aligned bam file. Corresponding bai index file must be in the same directory. |
Value
A data.frame containing a summary of the unique reads from bam file. Duplicate reads are defined as having identical pos and cigar values.
Author(s)
Nathaniel J. Madrid, Jason Byars
Examples
1 2 | BamFilePaths <- dir(path="/home/ubuntu/Projects/RNAseqPackage/bams", pattern=".*.bam$", full.names=T)
UniqueReadsDF = SummarizeUniqueReads(BamFilePaths[1])
|
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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