In sunnyeesl/BigLD: Big-LD

knitr::opts_chunk$set(echo = TRUE)

knitr::opts_chunk$set(
  fig.path = "README_figs/README-"
)

Big-LD

Big-LD is a block partition method based on interval graph modeling of LD bins which are clusters of strong pairwise LD SNPs, not necessarily physically consecutive. The detailed information about the Big-LD can be found in our paper published in bioinformatics.

Installation

library("devtools")
devtools::install_github("sunnyeesl/BigLD")

library(BigLD)

Data

You need an additive genotype data (each SNP genotype is coded in terms of the number of minor alleles) and a SNP information data. The package include sample genotype data and SNPinfo data.

Load the sample data (if you installed the BigLD packages).

data(geno)
data(SNPinfo)

Or simply you can download the sample data from /inst/extdata The sample data include 1000SNPs and 286 individuals.

geno[1:10, 1:7]
head(SNPinfo)

CLQD

CLQD partitioning the SNPs into subgroups such that each subgroup contains highly correlated SNPs. There are two CLQ methods, original CLQ(ClQmode = 'Maximal') and CLQD (ClQmode = 'Density').

CLQres = CLQD(geno, SNPinfo, CLQmode = 'Density')
head(CLQres, n = 20)

Big_LD

'Big_LD` returns the estimation of LD block regions of given data.

BigLDres = Big_LD(geno, SNPinfo)
BigLDres

If you want to apply heuristic procedure, add option checkLargest = TRUE.

Big_LD(geno, SNPinfo, MAFcut = 0.05, checkLargest = TRUE, appendrare = TRUE)

LDblockHeatmap

LDblockHeatmap visualize the LDblock boundaries detected by Big_LD.

You can input the results obtained using Big-LD (LDblockResult= BigLDres). If you do not input a Big-LD results, the LDblockHeatmap function first excute Big_LD function to obtain an LD block estimation result.

LDblockHeatmap(geno, SNPinfo, 22, LDblockResult= BigLDres)

You can show the location of the specific SNPs (showSNPs = SNPinfo[c(100, 200), ] shows the 100th and 200th SNPs), or give the threshold for LD block sizes to show SNP information (showLDsize = 50). If you want to save the LD heatmap results as tif file, add options such as savefile = TRUE, filename = "LDheatmap2.tif".

LDblockHeatmap(geno, SNPinfo, 22, showSNPs = SNPinfo[c(100, 200), ], showLDsize = 50, savefile = TRUE, filename = "LDheatmap2.tif")

LDblockres = LDblockHeatmap(geno, SNPinfo, 22, showSNPs = SNPinfo[c(100, 200), ], showLDsize = 50, savefile = TRUE, filename = "LDheatmap2.tif")

If you have any suggestion or question, please contact us ([e-mail]).

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