test_example.R

In cibiobcg/abemus: Adaptive Base Error Model in Ultra-Deep Sequencing Data

# For more information about the workflow please refer to the ABEMUS wiki page:
# https://github.com/cibiobcg/abemus/wiki/Usage
#
# Data available at: https://github.com/cibiobcg/abemus_models#test-dataset

library( devtools )
devtools::install_github("cibiobcg/abemus", build_vignettes = T)

library( abemus )
library( data.table )
library( parallel )

outdir <-  "~/test_dataset_abemus/"
sample.info.file <- "~/test_dataset_abemus/test_sif.tsv"
targetbed <- "~/test_dataset_abemus/regions.bed"
pacbamfolder <- "~/test_dataset_abemus/pacbam_data/"
pacbamfolder_bychrom <- "~/test_dataset_abemus/pacbam_data_bychrom/"

setwd(outdir)

# split pacbam outputs by chrom
split_pacbam_bychrom(targetbed = targetbed,
                     pacbamfolder = pacbamfolder,
                     pacbamfolder_bychrom = pacbamfolder_bychrom)

targetbp_list <- bed2positions(targetbed = targetbed,get_only_chromosomes = TRUE)

# compute per-base error model
outpbem <- compute_pbem(sample.info.file = sample.info.file,
                        targetbed = targetbed,
                        outdir=outdir,
                        pacbamfolder_bychrom=pacbamfolder_bychrom)

# outs
head( outpbem$pbem_tab )
outpbem$bperr_summary
outpbem$bgpbem
outpbem$mean_pbem

# compute coverage-based and not-coverage-based allelic fraction thresholds
outafth <- compute_afthreshold(outdir = outdir,
                               pbem_dir = file.path(outdir,"BaseErrorModel"))

# outs
head( outafth$th_results )
head( outafth$th_results_bin )
head( outafth$datacount_bin )

# call snvs in case samples
calls <- callsnvs(sample.info.file = sample.info.file,
                  controls_dir = file.path(outdir,"Controls"),
                  pbem_dir = file.path(outdir,"BaseErrorModel"),
                  detection.specificity = 0.995,
                  replicas = 10,
                  outdir=outdir,
                  outdir.calls.name = "Results",
                  targetbed = targetbed,
                  pacbamfolder_bychrom=pacbamfolder_bychrom)

head( calls$tabsnvs_index )

tabindex <- calls$tabsnvs_index

# compute mean coverage
tabindex <- get_case_mean_coverage(tabindex = tabindex,
                                   pacbamfolder_bychrom = pacbamfolder_bychrom)

target_size <- get_target_size(targetbed=targetbed, Mbp = TRUE)

# apply pbem scaling factor to calls
calls$tabsnvs_index_scalfact <- apply_scaling_factor(tabindex = tabindex,
                                                     target_size = target_size,
                                                     use.optimal.R = TRUE)

head( calls$tabsnvs_index_scalfact )