getNeighbours: getNeighbours

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

Description

Finds all genes within kb kilobases of genes listed in gvec according to data in sgd object, returned by readSGD.

Usage

getNeighbours(gvec,kb,sgd,geneCoord="Mid",geneDist="Mid",geneDir="All")

Arguments

gvec	Vector of gene names (systematic or standard gene names, or if you're lucky, aliases).
kb	Search range: search for genes whose centres are kb kilobases from centres of genes in gvec
sgd	Data frame representing features.tab file from SGD. As returned from readSGD.
geneCoord	Definition of position of target genes (from gvec). Options are: "Start", "Stop" and Mid" for the start, end and middle of the target gene respectively. Default value is "Mid".
geneDist	Gene feature used to define distance between target gene position and other genes on the same chromosome. Options are: "Start", "Stop", "Mid" (as for geneCoord) and "Min" which is the nearest out of "Start" and "Stop". Default value is "Mid".
geneDir	Direction from target in which to search for neighbouring genes. Options are: "Up", "Down" and "All" for just upstream, just downstream and both respectively. Default value is "All".

Value

Subset of rows from sgd dataframe containing information about genes/features within specified search range of genes in gvec. FName column contains systematic name of gene/features. Gene column contains standard name (where available).

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