comapr

Install

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("comapr")

Introduction

comapr is an R package for finding crossovers for SNP marker intervals by detecting haplotype shifts across groups of samples.

From marker genotyping results in data.frame

comapr can be applied for detecting crossovers from genotyping results of makers across samples in a marker by sample data.frame.

library(comapr)
head(snp_geno)
#>   CHR      POS       rsID C57BL.6J FVB.NJ..i.  X92 X93 X94 X95 X96 X97  X98
#> 1   1  4526088 rs13475701       GG         CC   CC  CC  CC  CC  CC  CC   CG
#> 2   1  5595513 rs13475705       TT         CC   CC  CC  CC  CC  CC  CC   CT
#> 3   1  6057774  rs3710263       CC         TT   TT  TT  TT  TT  TT  TT   TC
#> 4   1  6655964 rs13475709       CC         GG   GG  GG  GG  GG  GG  GG   CG
#> 5   1 21638464  rs6253968       TT         CC Fail  CC  CC  CC  CC  CC Fail
#> 6   1 22665060  rs6361963       AA         GG   AG  GG  GG  GG  GG  GG   AG
#>    X99 X100 X101 X102 X103 X104 X105 X106 X107 X108 X109 X110 X111 X112 X113
#> 1   CG   CC   CG   CG   CC   CG   CG   CC   CC   CC   CC   CG   CC   CC   CC
#> 2   CT   CC   CT   CT   CC   CT   CT   CC   CC   CC   CC   CT   CC   CC   CC
#> 3   TC   TT   TC   TC   TT   TC   TC   TT   TT   TT   TT   TC   TT   TT   TT
#> 4   CG   GG   CG   CG   GG   CG   CG   GG   GG   GG   GG   CG   GG   GG   GG
#> 5 Fail   CC   TC   TC   CC   CC   CC   CC   CC   CC Fail   TC   CC   CC   CC
#> 6   AG   GG   AG   AG   GG   GG   GG   AG   GG   GG   GG   AG   GG   GG   GG

From sgcocaller’s sparse matrices

comapr is also engineered to analyze the outputs from a single-sperm crossover calling tool sgcocaller

list.files("inst/extdata/")
#>  [1] "s1_barcodes.txt"        "s1_chr1_altCount.mtx"   "s1_chr1_snpAnnot.txt"  
#>  [4] "s1_chr1_totalCount.mtx" "s1_chr1_vi.mtx"         "s1_chr1_viSegInfo.txt" 
#>  [7] "s1_chr2_altCount.mtx"   "s1_chr2_snpAnnot.txt"   "s1_chr2_totalCount.mtx"
#> [10] "s1_chr2_vi.mtx"         "s1_chr2_viSegInfo.txt"  "s1_chr3_altCount.mtx"  
#> [13] "s1_chr3_snpAnnot.txt"   "s1_chr3_totalCount.mtx" "s1_chr3_vi.mtx"        
#> [16] "s1_chr3_viSegInfo.txt"  "s1_chr4_altCount.mtx"   "s1_chr4_snpAnnot.txt"  
#> [19] "s1_chr4_totalCount.mtx" "s1_chr4_vi.mtx"         "s1_chr4_viSegInfo.txt" 
#> [22] "s1_chr5_altCount.mtx"   "s1_chr5_snpAnnot.txt"   "s1_chr5_totalCount.mtx"
#> [25] "s1_chr5_vi.mtx"         "s1_chr5_viSegInfo.txt"  "s2_barcodes.txt"       
#> [28] "s2_chr1_snpAnnot.txt"   "s2_chr1_vi.mtx"         "s2_chr1_viSegInfo.txt" 
#> [31] "s2_chr2_snpAnnot.txt"   "s2_chr2_vi.mtx"         "s2_chr2_viSegInfo.txt" 
#> [34] "s2_chr3_snpAnnot.txt"   "s2_chr3_vi.mtx"         "s2_chr3_viSegInfo.txt" 
#> [37] "s2_chr4_snpAnnot.txt"   "s2_chr4_vi.mtx"         "s2_chr4_viSegInfo.txt" 
#> [40] "s2_chr5_snpAnnot.txt"   "s2_chr5_vi.mtx"         "s2_chr5_viSegInfo.txt"

Visualizing feature of single sperms

Crossover positions

Cumumative Genetic distances across intervals

Resampling methods for comparing groups

Analysis workflow for demonstration of comapr on a single-sperm DNAseq dataset

We demonstrate the usage of sgcocaller and comapr for identifying and visualising crossovers regions from single-sperm DNA sequencing dataset here