countAllReads: Read statistics
In jefferys/SamSeq: Work with aligned reads from a SAM file
Description
Usage
Arguments
Value
Description
Read statistics
Usage
1
countAllReads(x, ...)
Arguments
x
A Sam or SamReads object to return read statistics for.
Returns the number of lines of reads in the Sam file. Does no filtering, so
counts a multi-aligned read end once for each alignment and includes
duplicates, unaligned reads, failed QC alignments, etc. Can filter and then
re-apply to get any sub-scount desired. Dividing by 2 does not convert to
paired end results as some ends may match more or less times than another.
...
Required for S3 object method implementation. Not currently used.
Value
The total number of read records in the Sam file object.
jefferys/SamSeq documentation built on Oct. 25, 2019, 8:11 a.m.
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Description Usage Arguments Value
Description
Read statistics
Usage
1 | countAllReads(x, ...)
|
Arguments
x |
A Returns the number of lines of reads in the Sam file. Does no filtering, so counts a multi-aligned read end once for each alignment and includes duplicates, unaligned reads, failed QC alignments, etc. Can filter and then re-apply to get any sub-scount desired. Dividing by 2 does not convert to paired end results as some ends may match more or less times than another. |
... |
Required for S3 object method implementation. Not currently used. |
Value
The total number of read records in the Sam file object.
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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