chrWiseSplit: Split genome-wide genotyping data into separate files by...
In Junfang/Gimpute: Gimpute: An efficient genetic data processing and imputation pipeline
Description
Usage
Arguments
Value
Author(s)
Description
Split the whole genome genotyping data chromosome-wise; allow parallel computating for all chromosomes.
if chromosome 25 is also available, further split chr25 (PAR or Chr_XY) into PAR1 and PAR2 according to the genomic coordination GRCh37
from https://en.wikipedia.org/wiki/Pseudoautosomal_region.
The locations of the PARs within GRCh37 are:
PAR1 X 60001 2699520
PAR2 X 154931044 155260560
Usage
1
chrWiseSplit(plink, inputPrefix, chrX_PAR1suffix, chrX_PAR2suffix)
Arguments
plink
an executable PLINK program in either the current working directory or somewhere in the command path.
inputPrefix
the prefix of the input plink files before splitting.
chrX_PAR1suffix
if chromosome 25 is available and with PAR1, then generate the suffix with X_PAR1 for chrX_PAR1
chrX_PAR2suffix
if chromosome 25 is available and with PAR2, then generate the suffix with X_PAR2 for chrX_PAR2
outputPrefix
the prefix of the output plink files after splitting and the chromosome number will be appended separately.
Value
The output plink files for each chromosome and possibly also the suffix of chrX_PAR.
Author(s)
Junfang Chen <junfang.chen3@gmail.com>
Junfang/Gimpute documentation built on May 17, 2019, 10:11 p.m.
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Description Usage Arguments Value Author(s)
Description
Split the whole genome genotyping data chromosome-wise; allow parallel computating for all chromosomes. if chromosome 25 is also available, further split chr25 (PAR or Chr_XY) into PAR1 and PAR2 according to the genomic coordination GRCh37 from https://en.wikipedia.org/wiki/Pseudoautosomal_region. The locations of the PARs within GRCh37 are: PAR1 X 60001 2699520 PAR2 X 154931044 155260560
Usage
1 | chrWiseSplit(plink, inputPrefix, chrX_PAR1suffix, chrX_PAR2suffix)
|
Arguments
plink |
an executable PLINK program in either the current working directory or somewhere in the command path. |
inputPrefix |
the prefix of the input plink files before splitting. |
chrX_PAR1suffix |
if chromosome 25 is available and with PAR1, then generate the suffix with X_PAR1 for chrX_PAR1 |
chrX_PAR2suffix |
if chromosome 25 is available and with PAR2, then generate the suffix with X_PAR2 for chrX_PAR2 |
outputPrefix |
the prefix of the output plink files after splitting and the chromosome number will be appended separately. |
Value
The output plink files for each chromosome and possibly also the suffix of chrX_PAR.
Author(s)
Junfang Chen <junfang.chen3@gmail.com>
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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