rSNPdata

R package to manage and analyse Plasmodium falciparum whole genome SNPs data.

requirements

before installing this package, make sure the following tools are installed:

Index:

library(devtools)
devtools::install_github("FellouMada/rSNPdata", build_vignettes = TRUE)
library(rSNPdata)

browseVignettes("rSNPdata")

function name	description
get_snpdata	Create SNPdata onject. the functions in this package require a `SNPdata` object. This can be generated with this function
print	print the SNPdata object
compute_MAF	calculate the snp minor allele frequency based on the allelic depth and minor allele frequency
calculate_Fws	calculate the within-host genetic diversity index

function name	description
filter_snps_samples	filter loci and samples from the SNPdata object
select_chrom	select data for a provided list of chromosomes
drop_snps	remove a set of SNPs from the SNPdata object
drop_samples	remove a set of samples from the SNPdata object

function name	description
phase_mixed_genotypes	Phase mixed genotypes based on number of read supporting each allele and Bernoulli distribution. This process will be repeated `nsim` times and data from iteration with highest correlation between MAF phased data and MAF raw data will be retained
impute_missing_genotypes	impute missing genotypes based on minor allele frequency and Bernoulli distribution. This process will be repeated `nsim` times and data from iteration with highest correlation between MAF imputed data and MAF raw data will be retained

function name	description
calculate_wcFst	Calculate Weir & Cockerham's Fst. This is achieved using the vcflib tools
calculate_LD	Calculate LD R^2 between all pair of loci using vcftools
calculate_IBS	Calculate identity by state matrix
calculate_iR	Calculate the iR index between pairs of populations to determine loci with excess of IBD sharing. The calculation is based on the isoRelate R package
calculate_relatedness	Calculate relatedness between every pair od isolates for all pairs of population. This is based on the model developed by Aimee R. Taylor and co-authors