qfa.epiplot: Makes an epistasis plot from the full results of qfa.epi

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

Description

Creates a scatterplot of control fitnesses on the x-axis and query fitnesses on the y-axis, with those deemed to be hits (by FDR adjusted p-value) coloured. Essentially, this function assumes that the experiment consists of a series of paired fitness observations for a collection (typically genome-wide) of deletion mutations either single mutations (x-axis) or the same single mutation in combination with a common background or query mutation (y-axis). Fitting a linear regression to all observations (forced through the origin) and searching for significant deviations from that regression is equivalent to searching for mutations which show significant deviation from a multiplicative model of genetic interaction. Genes whose deletions deviate from this model significantly can be said to interact with the query gene.

Usage

qfa.epiplot(results,qthresh,fitratio=FALSE,ref.orf="YOR202W",xxlab="Control Fitness",
yylab="Query Fitness",mmain="Epistasis Plot",fmax=0)

Arguments

results	The results of interaction analysis returned by the qfa.epi function.
qthresh	The fdr adjusted cutoff point for determining hits.
fitratio	The ratio of background mutant fitness to wildtype fitness, from the genetic indepdence model. If FALSE, this is estimated from results using linear regression.
ref.orf	ORF for a reference strain (typically wild-type or a surrogate), whose fitness will be marked on the control and query axes of the interaction plot (horizontal and vertical blue lines). HIS3 is the default strain.
xxlab	x axis label
yylab	y axis label
mmain	Plot label
fmax	Maximum fitness range for both x-axis (control axis) and y-axis (query axis). If 0, axis ranges are automatically chosen to include all data points.

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