Description Usage Arguments Details Value Author(s) Examples
View source: R/convert.variants.to.numeric.R
Given a matrix or data frame with character ACGT SNP values, convert them to numeric values with the major allele coded as 0 and the minor allele as 1.
1 | convert.variants.to.numeric(variants)
|
variants |
Data frame with four header columns. The SNPs must be in ACGT format in columns 5 through ncol(snps). |
This function is used before calling plot.alleles() to convert the SNPs into a numeric form suitable for plotting.
Data.frame of the same dimentions as the snps argument, but with the alleles converted to 0 or 1.
Daniel Gatti
1 2 | data(example.snps)
numeric.snps = convert.variants.to.numeric(example.snps[1:100,])
|
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.