inst/buildScripts/chipTypes/HumanCytoSNP-12v2/HumanCytoSNP-12v2,ugp.R

In HenrikBengtsson/aroma.illumina: Analysis of Illumina microarray data [A DRAFT - TRUE]

if (interactive()) savehistory();
library("aroma.core");
verbose <- Verbose(threshold=-10, timestamp=TRUE);


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# Settings
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platform <- "Illumina";
chipType <- "HumanCytoSNP-12v2";
tags <- "HB20110924";

createdBy <- "Henrik Bengtsson (hb@biostat.ucsf.edu)";

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# Unit names mapping
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unf <- TextUnitNamesFile$byChipType(chipType, tags=tags);
print(unf);

unitNames <- getUnitNames(unf);
printf("Unit names:\n");
str(unitNames);


filename <- "marker_list_humancytoSNP12.txt";
db <- TabularTextFile(filename, path=getPath(unf));
print(db);


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# Allocate UNF file (gives an error if already exists)
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ugp <- AromaUgpFile$allocateFromUnitNamesFile(unf, tags=tags);

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# Import unit names
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patterns <- c("*"="NULL", Name="character", Chr="character", Position="integer");
data <- readDataFrame(db, colClassPatterns=patterns);

nbrOfUnits <- nrow(data);
printf("Number of units: %d\n", nbrOfUnits);

# Translate unit names to unit indices via UNF
units <- indexOf(unf, names=data[,"Name"]);
printf("Units:\n");
str(units);

# Sanity check
units <- Arguments$getIndices(units, max=nbrOfUnits(ugp));


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# Translate chromosome ids to chromosome indices
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map <- c(1:24);
names(map) <- map;
map <- c(map, X=23, Y=24, M=25, XY=26);
data[,"Chr"] <- map[data[,"Chr"]];
printf("Number of units per chromosome:\n");
print(table(data[,"Chr"]));


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# Write annotation data
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ugp[,1] <- data[,"Chr"];
ugp[,2] <- data[,"Position"];

ftr <- readFooter(ugp);
ftr$createdBy <- createdBy
ftr$srcFile <- list(filename=getFilename(db), filesize=getFileSize(db), checksum=getChecksum(db));
writeFooter(ugp, ftr);

print(ugp);