Man pages for FellouMada/rSNPdata
R package for Analysis of P. falciparum whole genome SNPs data
| calculate_Fws | Calculate the complexity of infection in every sample (Fws) |
| calculate_IBS | Generate dissimilarity matrix (1-IBS) between all pairs of... |
| calculate_iR | Calculate iR index to detect loci with excess of IBD sharing |
| calculate_LD | Calculate LD R^2 between pairs of loci |
| calculate_relatedness | Estimate the relatedness between pairs of isolates |
| calculate_wcFst | Calculate Weir & Cockerham's Fst |
| compute_MAF | Calculate minor allele frequency (MAF) |
| drop_samples | Drop samples |
| drop_snps | Drop set a SNPs |
| filter_snps_samples | Filter loci and samples (requires bcftools and tabix to be... |
| get_snpdata | Generate the SNPdata object |
| impute_missing_genotypes | Impute missing genotypes |
| phase_mixed_genotypes | Phase mixed genotypes |
| print.SNPdata | Print SNPdata |
| select_chrom | Select data from specified chromosomes |
