Description Usage Arguments Value
View source: R/filteringGenes.R
Finds all genes within kb kilobases of genes listed in gvec according to data in sgd object, returned by readSGD.
1 | getNeighbours(gvec,kb,sgd,geneCoord="Mid",geneDist="Mid",geneDir="All")
|
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". |
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).
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