map.to.roi: Map transcripts to ROI

In jleelab/leeplyr: A set of internal Lee lab tools ("plyers").

Description

Maps each individual transcripts to one or more region of interests (ROIs).

Usage

map.to.roi(transcripts, roi.folder = c(cytosol.folder, nuclei.folder),
  roi.labels = c("cytoplasm", "nucleus"), OR.cutoff = 5,
  p.value.cutoff = 20, plot = TRUE, roi.col = c("#C8EAEB", "#FCDAD1"),
  transcript.col = "black", cex = 0.2)

Arguments

transcripts	FISSEQ readr output tsv file path.
roi.folder	character vector, each element is the location of folder containing ImageJ roi files.
roi.labels	character vector, .
OR.cutoff	numeric, absolute OR value on log2 coordinates to use as cut-off. Default is 5.
p.value.cutoff	numeric, p-value on negative log10 coordinates to use as cut-off. Default is 20.
plot	boolean, plot output graph. Default is TRUE.
roi.col	character vector, Color of regions of interest. Default is c('#C8EAEB', '#FCDAD1').
transcript.col	character, color or transcripts in plot. Default is 'black'.
cex	numeric, Size of transcripts on plot showing alll transcripts. Default is 0.2.

Examples

cytosol.folder<-system.file('roi/RoiSet_cytosol', package='leeplyr')
nuclei.folder<-system.file('roi/RoiSet_nuclei', package='leeplyr')
transcripts<-system.file('fisseq/res_001_001FISSEQ.out', package='leeplyr')
map.to.roi(transcripts, roi.folder = c(cytosol.folder, nuclei.folder), roi.labels =  c('cytoplasm', 'nucleus'), OR.cutoff = 5, p.value.cutoff = 20)

jleelab/leeplyr documentation built on May 3, 2019, 9:38 p.m.