baf_stats: baf_stats
In knausb/coveRage: Tools to Explore Sequencing Coverage in High-Throughput Sequencing Projects
Description
Usage
Arguments
Details
Description
Convert mpileup output to count tables
Usage
1
baf_stats(inMatrix, minq = 0L)
Arguments
inMatrix
input matrix
minq
minimum quality for call to be retained
Details
The character matrix inMatrix should consist of columns 5 columns.
The first column is the chromosome name (and is not presently used).
The second column is the chromosomal position.
The third column is the reference allele.
The fourth column is a string of calls.
The fifth column is a string of qualities.
This is expected to come from mpileup output.
Note that while mpileup can include data for multiple samples, here we need to process each sample seperately.
The reference alleles must be in all upper case.
See toupper if they are not.
knausb/coveRage documentation built on May 20, 2019, 12:52 p.m.
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Description Usage Arguments Details
Description
Convert mpileup output to count tables
Usage
1 | baf_stats(inMatrix, minq = 0L)
|
Arguments
inMatrix |
input matrix |
minq |
minimum quality for call to be retained |
Details
The character matrix inMatrix should consist of columns 5 columns. The first column is the chromosome name (and is not presently used). The second column is the chromosomal position. The third column is the reference allele. The fourth column is a string of calls. The fifth column is a string of qualities. This is expected to come from mpileup output. Note that while mpileup can include data for multiple samples, here we need to process each sample seperately.
The reference alleles must be in all upper case.
See toupper if they are not.
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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