Question: FW: How to plot microRNA chromosome location
gravatar for Dykema, Karl
11.1 years ago by
Dykema, Karl90
Dykema, Karl90 wrote:
Hello Bioc users, While our package idiogram is has been created to primarily display gene expression data (with an associated chromLocation object) you can alternatively create one on the fly. In the code below I create a mock data frame similar to Camper's and from that I generate a bare bones chromLocation object. From there you can plot the data a couple of different ways. Feel free to ask further questions or offer suggestions. Thanks! ------------------------------------------- Karl Dykema Computational Biologist Van Andel Research Institute 333 Bostwick Ave NE Grand Rapids, MI 49503 ## load idiogram package library(idiogram) ## create mock data object data <- data.frame(miRNA=c("hsa-miR-130b","hsa-miR-33a","hsa-miR-15b1 ","hsa-miR-15b2","hsa-miR-15b3","hsa-miR-15b4"), chrom=c("1","1","4","5","6","13"), start=c(20337592,40626894,161605069,28337592,30337592,337592)) ## create chromLocation object genome <- new("chromLocation") start <- data[,"start"] names(start) <- data[,"miRNA"] genome at chromLocs <- new("list",tapply(start,factor(data[,"chrom"]),I)) genome at organism <- "Homo Sapiens" ## create vector of mock data toPlot <- rep(1,length(data$miRNA)) names(toPlot) <- data$miRNA ## plot with cytobands represented by tick marks idiogram(toPlot,genome,"1",type="p",xlim=c(0,2)) ## plot with cytobands represented by an image of an idiogram idiogram(toPlot,genome,"1",type="p",xlim=c(0,2),margin="i") This email message, including any attachments, is for th...{{dropped:6}}
organism idiogram • 531 views
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