tardbpdms_dimsumcounts_to_fitness: tardbpdms_dimsumcounts_to_fitness

In lehner-lab/tardbpdms: Analysis scripts for processing TDP-43 DMS data from Bolognesi et al. 2019.

Description

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

Usage

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.