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title: Fetch Windram et al. data author: John Reid output: html_document
library(knitr) library(rmarkdown) # # knitr options # opts_chunk$set( fig.path = 'figures/Windram-', stop_on_error = TRUE, fig.width = 12.5, fig.height = 8)
library(rmarkdown) library(devtools) load_all('../..') render('fetch-Windram.Rmd')
library(dplyr) # suppressMessages(loadfonts()) # # Stylesheet # options(markdown.HTML.stylesheet = system.file("inst/Rmd/foghorn.css", package="DeLorean"))
Windram et al. investigated the defense response in Arabidopsis thaliana to the necrotrophic fungal pathogen Botrytis cinerea.
# library(dplyr) # source("http://bioconductor.org/biocLite.R") # biocLite("GEOquery") library(GEOquery) gse <- getGEO("GSE29642", GSEMatrix=TRUE)[[1]] show(gse) length(gse) # Expression data class(exprs(gse)) dim(exprs(gse)) # Phenotypic data dim(pData(gse)) class(pData(gse)) names(pData(gse)) windram.expr <- exprs(gse) colnames(windram.expr) windram.gene.meta <- data.frame( gene=rownames(windram.expr), TAIR9=fData(gse)$TAIR9_best) windram.cell.meta <- data.frame( cell=pData(gse)$geo_accession, # title=pData(gse)$title, obstime=as.numeric(str_match(pData(gse)$title, "[[:digit:]]+")), condition=str_match(pData(gse)$title, "^Mock|Botrytis") ) %>% mutate(capture=factor(as.character(obstime), ordered=TRUE, levels=unique(as.character(obstime)))) windram.cell.meta levels(windram.cell.meta$capture)
Add gene names mentioned in the text (Supplemental Table 2) to the meta data and remove other genes from expression data.
text.genes <- c( "AT1G65060", "AT3G51240", "AT1G49720", "AT5G46330", "AT4G26080", "AT1G74590", "AT5G57050", "AT1G78380", "AT5G64750", "AT1G17170", "AT1G01780", "AT1G17180", "AT4G11280", "AT2G29470", "AT1G06080", "AT2G29420", "AT1G01720", "AT3G09270", "AT1G52890", "AT3G59400", "AT3G15500", "AT3G14930", "AT5G08790", "AT2G40490", "AT5G39610", "AT2G44950", "AT1G13280", "AT1G74710", "AT2G45220", "AT1G19180", "AT5G05730", "AT1G17380", "AT1G25220", "AT4G22880", "AT2G31230", "AT1G55020", "AT3G62770", "AT1G17420", "AT5G45900", "AT1G72520", "AT4G21980", "AT5G23010", "AT4G04620", "AT3G18690", "AT1G03850", "AT3G45640", "AT3G53980", "AT4G01370", "AT5G05960", "AT2G43790", "AT1G18300", "AT3G06490", "AT3G27310", "AT1G06180", "AT5G64080", "AT2G47190", "AT2G13820", "AT5G61420", "AT3G19580", "AT5G07690", "AT4G33430", "AT5G12870", "AT3G19710", "AT1G18570", "AT2G39660", "AT1G73410", "AT4G39400", "AT5G56110", "AT3G13380", "AT1G32640", "AT2G46830", "AT2G34720", "AT3G21630", "AT4G14540", "AT4G32410", "AT1G09030", "AT5G05170", "AT1G56170", "AT5G45340", "AT1G64280", "AT2G30770", "AT5G45110", "AT1G16400", "AT3G50410", "AT4G13770", "AT1G07640", "AT5G25350", "AT3G55370", "AT4G39030", "AT1G06160", "AT3G23240", "AT3G26830", "AT3G15210", "AT3G22231", "AT5G47230", "AT3G11820", "AT4G17490", "AT1G09530", "AT5G61270", "AT2G14610", "AT5G64900", "AT5G53160", "AT1G01360", "AT4G17870", "AT3G14230", "AT3G01650", "AT5G14420", "AT2G22990", "AT5G66880", "AT3G51060", "AT5G06850", "AT1G22070", "AT5G06960", "AT3G12250", "AT3G02140", "AT3G21780", "AT5G24780", "AT5G55120", "AT4G31800", "AT2G03340", "AT2G38470", "AT1G13960", "AT1G80840", "AT1G62300", "AT4G23810", "AT2G25000", "AT3G56400", "AT5G13080", "AT5G46350") windram.gene.meta <- windram.gene.meta %>% filter(TAIR9 %in% text.genes) windram.expr <- windram.expr[windram.gene.meta$gene,] dim(windram.expr)
Save the data in a format suitable for DeLorean package.
save(windram.expr, windram.gene.meta, windram.cell.meta, file='../../data/WindramDeLorean.rda')
R version and packages used:
sessionInfo()
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