normalisesnp: Normalise SNPs according to a reference frequency under a...
In danjlawson/pcapred: Produce PC Eigenvector Predictions From Plink Input Data And Loadings
Description
Usage
Arguments
Value
Description
Normalise a SNP count vector for a single SNP by an external reference frequency distribution by mean and standard deviation predicted under a binomial model.
Usage
1
normalisesnp(x, f, ploidy = 2, minfreq = 0.001, meanimpute = FALSE)
Arguments
x
A vector of Individuals SNP data of length N
f
The snp frequency for that SNP
ploidy
ploidy of the data (2=diploid) ; maximum that rawdatmat can take
minfreq
a thresholding for very raw SNPs in the reference, to prevent them from being over-weighted
meanimpute
(default FALSE) whether to mean impute missing data
Value
A vector of length = length(x)
danjlawson/pcapred documentation built on Oct. 7, 2021, 3:47 p.m.
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Description Usage Arguments Value
Description
Normalise a SNP count vector for a single SNP by an external reference frequency distribution by mean and standard deviation predicted under a binomial model.
Usage
1 | normalisesnp(x, f, ploidy = 2, minfreq = 0.001, meanimpute = FALSE)
|
Arguments
x |
A vector of Individuals SNP data of length N |
f |
The snp frequency for that SNP |
ploidy |
ploidy of the data (2=diploid) ; maximum that rawdatmat can take |
minfreq |
a thresholding for very raw SNPs in the reference, to prevent them from being over-weighted |
meanimpute |
(default FALSE) whether to mean impute missing data |
Value
A vector of length = length(x)
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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