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TrypLik

The goal of TrypLik is to support tryptase copy number estimation from sequence data.

Installation instructions

Get the latest stable R release from CRAN.

Install the development version from GitHub with:

BiocManager::install("HIBio/TrypLik")

or, if not using the Bioconductor ecosystem:

remotes::install_github("HIBio/TrypLik")

Preprocessing

Provided the sequencing data has been processed (see the background vignette included in this package, and accompanying shell scripts in inst/) to produce the reads mapped to specific tryptase alleles, these can be provided to the TrypLik function

library("TrypLik")

TrypLik(26, 0, 347, 316, 304)
#>   Alpha_count Beta_count Beta_FS_count Posterior_likelihood
#> 1           2          2             0              0.99890
#> 2           2          3             0              0.00008
#> 3           3          2             0              0.00082
#> 4           3          3             0              0.00020

This function is an R wrapper for the C function, producing a native data.frame.

The C code is provided as a standalone source file in inst/tryplik.c in which the R-related code has been commented out. The R wrapper uses the file src/tryplik.c which only differs in the additional R components.

Once compiled, the standalone version can be used in a command-line pipeline; following the processing outlined in the background vignette, one could use

[...]
samtools markdup -r positionsort.sam temp.sam
./count_tryptase >> tryptase.out

cat tryptase.out | awk '{printf "./Tryplik %d %d %d %d %d | sort -nk2 | tail -n 1\n", $6, $7, $8, $9, $10}'

The processing can be entirely performed from R, provided that both samtools and bwa are installed. To preprocess the file HG00100.final.cram from 1000 Genomes, producing a .sam file suitable for counting

sam_file <- preprocess("HG00100.final.cram")
# Processing... this may take some time
# [bwa_index] Pack FASTA... 0.00 sec
# [bwa_index] Construct BWT for the packed sequence...
# [bwa_index] 0.00 seconds elapse.
# [bwa_index] Update BWT... 0.00 sec
# [bwa_index] Pack forward-only FASTA... 0.00 sec
# [bwa_index] Construct SA from BWT and Occ... 0.00 sec
# [main] Version: 0.7.17-r1188
# [main] CMD: bwa index consensus.fa
# [main] Real time: 0.004 sec; CPU: 0.004 sec
# [M::bam2fq_mainloop] discarded 228 singletons
# [M::bam2fq_mainloop] processed 27228 reads
# [M::bwa_idx_load_from_disk] read 0 ALT contigs
# [M::process] read 27000 sequences (4050000 bp)...
# [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 1190, 0, 0)
# [M::mem_pestat] skip orientation FF as there are not enough pairs
# [M::mem_pestat] analyzing insert size distribution for orientation FR...
# [M::mem_pestat] (25, 50, 75) percentile: (348, 429, 530)
# [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 894)
# [M::mem_pestat] mean and std.dev: (422.49, 140.29)
# [M::mem_pestat] low and high boundaries for proper pairs: (1, 1076)
# [M::mem_pestat] skip orientation RF as there are not enough pairs
# [M::mem_pestat] skip orientation RR as there are not enough pairs
# [M::mem_process_seqs] Processed 27000 reads in 1.101 CPU sec, 1.064 real sec
# [main] Version: 0.7.17-r1188
# [main] CMD: bwa mem consensus.fa tempR1.fastq tempR2.fastq
# [main] Real time: 1.097 sec; CPU: 1.133 sec
# result file temp.sam is here: temp.sam

sam_file
# [1] "temp.sam"

counts <- count_tryptase(sam_file)
counts
# [1]  24   0  22   0  26   0 347 316 304

TrypLik(counts)
#   Alpha_count Beta_count Beta_FS_count Posterior_likelihood
# 1           2          2             0              0.99890
# 2           2          3             0              0.00008
# 3           3          2             0              0.00082
# 4           3          3             0              0.00020

(the TrypLik function takes either a single vector of counts or values provided to specific arguments).

Citation

Below is the citation output from using citation('TrypLik') in R. Please run this yourself to check for any updates on how to cite TrypLik.

print(citation("TrypLik"), bibtex = TRUE)
#> Warning in citation("TrypLik"): no date field in DESCRIPTION file of package
#> 'TrypLik'
#> Warning in citation("TrypLik"): could not determine year for 'TrypLik' from
#> package DESCRIPTION file
#> 
#> To cite package 'TrypLik' in publications use:
#> 
#>   Carroll J, Wall J (????). _TrypLik: Calculates Tryptase Variant
#>   Likelihoods_. R package version 0.1.0.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {TrypLik: Calculates Tryptase Variant Likelihoods},
#>     author = {Jonathan Carroll and Jeff Wall},
#>     note = {R package version 0.1.0},
#>   }

Please note that the TrypLik was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the TrypLik project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

This package was developed using biocthis.