abetadms_preprocess_fitness: abetadms_preprocess_fitness

In lehner-lab/abetadms: Analysis scripts for processing Abeta DMS data

Description

Estimate fitness of doubles mutants using bayesian framework from DiMSum fitness output.

Usage

abetadms_preprocess_fitness(fitness_path, outpath, all_reps,
  bayesian_double_fitness = F, min_mean_input_read_count = 10,
  min_input_read_count_doubles = 50, lam_d = 0.025, numCores = 10,
  execute = TRUE)

Arguments

fitness_path	path to DiMSum output (required)
outpath	output path for plots and saved objects (required)
all_reps	list of replicates to retain (required)
bayesian_double_fitness	Estimate fitness of double mutants using bayesian framework (default:F)
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/abetadms documentation built on April 16, 2020, 11:50 a.m.