cssFile <- system.file("extdata", "style.css", package="ccPaper") options(markdown.HTML.stylesheet = cssFile)
One of the experimental data sets we use is from [GEO][http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18842]. This documents the actual processing.
download.file("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE18nnn/GSE18842/matrix/GSE18842_series_matrix.txt.gz", "/mlab/data/rmflight/Documents/projects/work/ccPaper/otherData/GSE18842_series_matrix.txt.gz")
library(GEOquery) lung <- getGEO(filename="otherData/GSE18842_series_matrix.txt.gz") tmpP <- pData(lung) tmpP <- tmpP[,c("title", "geo_accession", "platform_id", "data_processing", "supplementary_file", "source_name_ch1", "characteristics_ch1", "characteristics_ch1.1")] pData(lung) <- tmpP tmpF <- fData(lung) tmpF <- tmpF[, c("ID", "GB_ACC", "SPOT_ID", "Annotation Date", "Sequence Type", "Sequence Source", "Target Description", "Representative Public ID", "Gene Title", "Gene Symbol", "ENTREZ_GENE_ID", "RefSeq Transcript ID")] fData(lung) <- tmpF save(lung, file="inst/data/lung.RData", compress="xz")
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