calculateFitnessScores: Calculate Fitness Scores
In RachelSilverstein/BioTools: Tools for bio computing

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/calculateFitnessScores.R

Calculate fitness scores of variants from raw DMS data.

1	calculateFitnessScores(DMS_data, nonselect_cutoff = 200)

`DMS_data`	Data frame FOR A SINGLE GENE of the form output by `readDMS`
`nonselect_cutoff`	Filter out low confidence variants with less than this many reads per million in nonselective conditions. (Default is 200 reads per million)

A more detailed description of what the function does.

Input data frame plus the following columns: select (the average of select1 and select2), nonselect (the average of nonselect1 and nonselect2), fold_change, fitness_score

Rachel Silverstein (aut)

readDMS The output of this function should be used as input for calculateFitnessScores.

# this example only works on my computer
setwd("/Users/Rachel/desktop/Roth Lab/R_DMS")
path <- './data/rawData_UBE2I_solid.txt'
gene_name <- 'UBE2I'
raw_data <- readDMS(path, gene_name)
head(calculateFitnessScores(raw_data))