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getDeadLocations<-function(SGAFile,SGAExpt,CutoffFrac=0.0025){
# Read in the SGA Colonyzer file
sga=read.delim(SGAFile,sep="\t",header=FALSE,stringsAsFactors=FALSE)
colnames(sga)=c("FILENAME","ROW","COLUMN","TOPLEFTX","TOPLEFTY","WHITEAREA","TRIMMED","THRESHOLD","INTENSITY","EDGEPIXELS","COLR","COLG","COLB","BKR","BKG","BKB","EDGELEN","XDIM","YDIM")
# Create barcode and date columns
sga$BARCODE=substr(sga$FILENAME,1,11)
sga$DATETIME=substr(sga$FILENAME,13,31)
# Read in the SGA Experimental desciption file
expt=read.delim(SGAExpt,sep="\t",header=TRUE,stringsAsFactors=FALSE)
# Using row.names speeds up indexing..?
row.names(expt)=expt$Barcode
getPlate<-function(barc) expt[barc,]$PlateNumber
getLib<-function(barc) expt[barc,]$Library
# Fill in the plate numbers and library names
sga$PLATE=sapply(sga$BARCODE,getPlate)
sga$LIBRARY=sapply(sga$BARCODE,getLib)
# Fill in the repeat numbers for 384 format
sga$REP384=((sga$COLUMN-1)%%2+1)+2*((sga$ROW-1)%%2)
# Fill in the row and column numbers for 384 format
sga$ROW384=ceiling(sga$ROW/2)
sga$COLUMN384=ceiling(sga$COLUMN/2)
# Now we can define what we mean by "dead" pinned SGA cultures
# Get average tile dimensions
xdim=mean(sga$XDIM)
ydim=mean(sga$YDIM)
minfit=CutoffFrac*xdim*ydim*255
sgadead=sga[sga$TRIMMED<minfit,]
return(sgadead)
}
#SGAFile='CDC13-1EXO1/IMAGELOGS/SGAFinal.dat'
#SGAExpt='CDC13-1EXO1/AUXILIARY/SGAExptDescription.txt'
#strip=getDeadLocations(SGAFile,SGAExpt)
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