tardbpdms_dimsumcounts_to_fitness: tardbpdms_dimsumcounts_to_fitness

Description Usage Arguments Value

View source: R/tardbpdms_dimsumcounts_to_fitness.R

Description

Estimate fitness of singles, doubles and silent AA substitution variants from DiMSum formatted output counts.

Usage

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tardbpdms_dimsumcounts_to_fitness(counts_path, outpath, generations_path,
  all_reps, min_mean_input_read_count = 10,
  min_input_read_count_doubles = 50, lam_d = 0.025, numCores = 1,
  execute = TRUE)

Arguments

counts_path

path to DiMSum output (required)

outpath

output path for plots and saved objects (required)

generations_path

path to generations data (required)

all_reps

list of replicates to retain (required)

min_mean_input_read_count

minimum mean input read count for high confidence variants (default:10)

min_input_read_count_doubles

minimum input read count for doubles used to derive prior for Bayesian doubles correction (default:50)

lam_d

Poisson distribution for score likelihood (default:0.025)

numCores

Number of available CPU cores (default:1)

execute

whether or not to execute the analysis (default: TRUE)

Value

Nothing


lehner-lab/tardbpdms documentation built on July 19, 2019, 7:24 p.m.