LDblockHeatmap: Draw LDblock results on LD heatmap.

In sunnyeesl/BigLD: Big-LD

Draw LDblock results on LD heatmap.

Description

LDblockHeatmap shows the LDblock regions obtained by Big-LD algorithm.

Usage

LDblockHeatmap(geno, SNPinfo, chrN, showSNPs = NULL, LDblockResult = NULL,
  tick = c("bp", "rsID"), st.bp = 0, ed.bp = Inf, showLDsize = 3,
  savefile = FALSE)

Arguments

geno	A data frame or matrix of additive genotype data, each column is additive genotype of each SNP.
SNPinfo	A data frame or matrix of SNPs information. 1st column is rsID and 2nd column is bp position.
chrN	A integer value to specify chromosome number of the given data.
showSNPs	A data frame which is part of SNPinfo that you want to show in the result LDblock heatmap. The default is NULL
LDblockResult	A data frame obtained by Big_LD function. If NULL(default), the GPART function first excute Big_LD function to obtain LD blocks estimation result.
tick	A character string to specify how to show first SNPs and last SNPs of LD blocks, in "bp" or in "rsID".
st.bp	A integer value to specify starting bp position of the region to draw.
ed.bp	A integer value to specify end bp position of the region to draw.
showLDsize	A integer value to specify the size (number of SNPs) of LDblocks to show ticks. if showLDsize = k, then blocks of size equal or greater than k is shown with boundaries and the "rsID" or "bp" of the first and last SNPs, however, the blocks whose size is less than k is shown with only boundaries.
savefile	logical. If TRUE, save tif file into work directory and the file is named after the chromosome and the physical range to draw. The default is FALSE

Value

A grid graphical object of LD block heatmap. The LD block heatmap will be presented on the screen after execution of the function. #'

Author(s)

Sun-Ah Kim <[e-mail]>, Yun Joo Yoo <[e-mail]>

See Also

Big_LD

Examples

data(geno)
data(SNPinfo)
LDblockHeatmap(geno, SNPinfo,chrN = 22, showSNPs = NULL)
LDblockHeatmap(geno, SNPinfo, 22, showSNPs = SNPinfo[c(100, 200), ], showLDsize = 10, savefile = TRUE)

sunnyeesl/BigLD documentation built on July 11, 2022, 8:01 a.m.