getMissingGenotypes: getMissingGenotypes

In qfa: Tools for Quantitative Fitness Analysis (QFA) of Arrayed Microbial Cultures Growing on Solid Agar Surfaces

Description

For a given list of QFA numbers, finds all of the genotypes which we can classify as being missing in the first stage of each of the SGAs that preceded genome-wide QFA. We can assume that genotypes which are missing in the first stage of an SGA (where stains are not under marker-specific selection) are simply missing from the library (rather than synthetic lethal interaction with background mutation for example). Cultures with a specific genotype are classified as being missing if their fitness is less than thresfrac times the median fitness of all genotypes observed in that screen.

Usage

getMissingGenotypes(QFAs,threshfrac,mer)

Arguments

QFAs	List of QFA numbers to examine.
threshfrac	Genotypes whose median fitness is less than thresfrac times the genome-wide median will be classified as dead.
mer	Data frame representation of Lydall lab database file (as returned by readMer).

Value

Subset of rows from fitness reports containing information about genotypes classified as missing. ORF column contains systematic gene names. Gene column contains standard gene names.

qfa documentation built on Feb. 22, 2020, 3:01 a.m.