subset_downsize {copyseparator} | R Documentation |
subset_downsize
Description
Subdivides the imported read alignment into subsets and then downsizes each subset by deleting those sequences that have too many gaps or missing data.
Usage
subset_downsize(filename, read_length, overlap, verbose = 1)
Arguments
filename |
A fasta file contains thousands of short reads that have been mapped to a reference. The reference and reads that are not directly mapped to the reference need to be removed after mapping. |
read_length |
An integer (e.g. 250, or 300) giving the read length of your Next-generation Sequencing data. This method is designed for read length >=250bp. |
overlap |
An integer describing number of base pairs of overlap between adjacent subsets. More overlap means more subsets. |
verbose |
Turn on (verbose=1; default) or turn off (verbose=0) the output. |
Value
A number of overlapping subsets (before and after downsizing) of the input alignment.
Examples
## Not run:
subset_downsize("inst/extdata/toydata.fasta",300,225,1)
## End(Not run)
[Package copyseparator version 1.2.0 Index]