Description Usage Arguments Value Author(s) References Examples
Genotype clustering and calling for Illumina microarrays.
1 2 3 |
indata |
A list containing input data on one or all SNPs, and would normally be produced by the function |
p |
A positive integer specifying which SNP to cluster. The default is 1. |
priorfrac |
A non-negative scalar specifying the number of observations, as a fraction of the number of samples N, of pseudodata to be appended to the heterozygous and homozygous minor genotypes. The default is 0.2. |
uncertcutoff |
Genotype calls with uncertainty greater than |
qcutoff |
Uncertainty scores lower than the |
showplots |
A logical value. If TRUE, the function will produce a series of plots. The default is FALSE. |
xm1, xm2, xm3, ym1, ym2, ym3 |
Pseudodata cluster means can be user-specified through these parameters. The ordered pair (xm1,ym1) gives the cluster mean for genotype AA; similarly for (xm2,ym2), (xm3,ym3) and AB, BB, respectively. Default values are NA, in which case cluster means are estimated from the data, conditional on the a priori genotypes produced by GenomeStudio. |
ranseed |
Random seed for generation of pseudodata. The default is 1969. |
R.lowcutoff |
Genotypes for which R is less than R.lowcutoff are set to "NC" (no call). The default is 0.05. |
A list with the following components:
calls |
A data frame with N rows and 4 columns, namely, |
snp |
The SNP name (i.e. rs-number). |
callrate |
Call rate for the SNP. |
priorfrac |
Value of argument in function call. |
uncertcutoff |
Value of argument in function call. |
qcutoff |
Value of argument in function call. |
Stephen W. Erickson serickson@rti.org with Joshua C. Callaway joshcllw@gmail.com
Stephen W. Erickson, Joshua Callaway (2016). SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays. Journal of Statistical Software, 71(2), 1-9. doi:10.18637/jss.v071.c02
1 2 3 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.