haploblock_df2list: convert a haploblock-defining data frame to a list

In PolyHaplotyper: Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids

Description

convert a haploblock-defining data frame to a list as needed by inferHaplotypes

Usage

haploblock_df2list(df, mrkcol, hbcol, sorted=TRUE)

Arguments

df	a data.frame with at least the following two columns
mrkcol	the name or number of the column with the markers
hbcol	the name or number of the column with the haploblocks
sorted	if TRUE (default) the haploblock list is sorted in alphabetical order of haploblock name (the markers within haploblocks are not sorted); if FALSE the haploblocks will be in order of first occurrence in df

Details

function inferHaplotypes needs a list where each item is a vector of all markers in one haploblock. This function produces such a list from a data.frame where the markers are in one column and the haploblocks in another column. The markers and haploblocks columns may be character, factor or numeric, and the columns may be indicated by name or number.

Value

the desired list

Examples

df1 <- data.frame(
 marker=paste0("mrk",1:9),
 block=LETTERS[c(1,2,3,2,3,1,1,2,2)],
 extracol=runif(9))
haploblock_df2list(df=df1, mrkcol="marker", hbcol=2)

PolyHaplotyper documentation built on June 17, 2021, 5:12 p.m.