make_it_012: just a quick function for making an 012 matrix from a...
In whoa: Evaluation of Genotyping Error in Genotype-by-Sequencing Data
Description
Usage
Arguments
Value
Examples
Description
The standard way within R of pulling values out of a named
vector really bogs down on large data sets. So I will do this instead.
Usage
1
make_it_012(M)
Arguments
M
a character matrix of variant call format (VCF) genotypes and no dimnames. Allowable values are
"0/0", and "0|0", which get coverted to integer 0; "0/1", "0|1", "1/0", and "1|0",
which get converted to integer 1; and
"1/1", and "1|1", which get converted to integer 2. Everything else gets
converted to -1 to denote missing data.
Value
An integer matrix of values which are 0, 1, 2, or -1.
Examples
1
2
3
4
# get an 012 matrix from the lobster data
tmp <- t(vcfR::extract.gt(lobster_buz_2000, element = "GT"))
dimnames(tmp) <- NULL
g <- make_it_012(tmp)
whoa documentation built on Aug. 11, 2021, 9:06 a.m.
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Description Usage Arguments Value Examples
Description
The standard way within R of pulling values out of a named vector really bogs down on large data sets. So I will do this instead.
Usage
1 | make_it_012(M)
|
Arguments
M |
a character matrix of variant call format (VCF) genotypes and no dimnames. Allowable values are "0/0", and "0|0", which get coverted to integer 0; "0/1", "0|1", "1/0", and "1|0", which get converted to integer 1; and "1/1", and "1|1", which get converted to integer 2. Everything else gets converted to -1 to denote missing data. |
Value
An integer matrix of values which are 0, 1, 2, or -1.
Examples
1 2 3 4 | # get an 012 matrix from the lobster data
tmp <- t(vcfR::extract.gt(lobster_buz_2000, element = "GT"))
dimnames(tmp) <- NULL
g <- make_it_012(tmp)
|
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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