csvname="CCLE_NP24.2009_Drug_data_2012.02.20.csv"
csvhash.md5="b64295ef99912d1d4bead76461d0e2a1"
parseCCLEline = function(dfline, validateNames=FALSE) {
# parse a row of ccle CSV import
if (nrow(dfline)!=1 || !is.data.frame(dfline))
stop("input must be 1line data.frame")
jan2013names = c("CCLE.Cell.Line.Name", "Primary.Cell.Line.Name", "Compound",
"Target", "Doses..uM.", "Activity.Data..median.", "Activity.SD",
"Num.Data", "FitType", "EC50..uM.", "IC50..uM.", "Amax", "ActArea"
)
if (validateNames && !isTRUE(all.equal(names(dfline), jan2013names)))
warning("it appears the names of the input data.frame do not agree with expectation")
getOrgan = function(x) {x = sub("_", "@@", x); gsub(".*@@", "", x) }
cvec = as.character(dfline)
cvec[cvec=="NA"] <- NA
new("ccleExpt",
organ=getOrgan(cvec[1]),
line=cvec[2], compound=cvec[3],
target = cvec[4], doses_uM=.nstring2vec(cvec[5]),
activityMedian=.nstring2vec(cvec[6]),
activitySD=.nstring2vec(cvec[7]),
fitType=cvec[9],
EC50_uM = as.numeric(cvec[10]),
IC50_uM = as.numeric(cvec[11]),
Amax = as.numeric(cvec[12]),
ActArea = as.numeric(cvec[13]))
}
#df = read.csv(csvname, h=TRUE, stringsAsFactors=FALSE)
#nr = nrow(df)
#recs = lapply(1:nr, function(x) parseCCLEline(df[x,]))
#ccle = new("ccleSet", expts=recs, dateCreated=date(),
# csvname=csvname, csvhash.md5=csvhash.md5)
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