Nothing
if (interactive()) savehistory();
library("aroma.affymetrix");
log <- Verbose(threshold=-10, timestamp=TRUE);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Settings
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
naVersion <- "26";
user <- "HB";
datestamp <- "20080723";
chipType <- "GenomeWideSNP_5";
cdfTags <- "Full,r2";
nbrOfEnzymes <- 2;
chipType6 <- "GenomeWideSNP_6,Full";
footer <- list(
createdOn = format(Sys.time(), "%Y%m%d %H:%M:%S", usetz=TRUE),
createdBy = list(
fullname = "Henrik Bengtsson",
email = sprintf("%s@%s", "henrik.bengtsson", "aroma-project.org")
),
srcFiles = list()
);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup required annotation files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (!exists("cdf")) {
cdf <- AffymetrixCdfFile$byChipType(chipType, tags=cdfTags);
rm(csvList);
}
print(cdf);
if (!exists("cdf6")) {
cdf6 <- AffymetrixCdfFile$byChipType(chipType6);
}
print(cdf6);
if (!exists("ufl6")) {
ufl6Tags <- sprintf("na%s", naVersion);
ufl6 <- AromaUflFile$byChipType(getChipType(cdf6), tags=ufl6Tags);
}
print(ufl6);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup UFL file
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
tags <- sprintf("na%s+,%s%s", naVersion, user, datestamp);
if (!exists("ufl")) {
ufl <- AromaUflFile$byChipType(getChipType(cdf), tags=tags);
}
print(ufl);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Import from the GWS6 file
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Identify units with missing UFL data
isMissing <- (is.na(ufl[,1]) & is.na(ufl[,2]));
print(summary(drop(isMissing)));
## Mode FALSE TRUE
## logical 752478 168450
units <- which(isMissing);
unitNames <- getUnitNames(cdf, units=units);
# Identify which exists in GWS6
units6 <- match(unitNames, getUnitNames(cdf6));
keep <- is.finite(units6);
print(summary(keep));
## Mode FALSE TRUE
## logical 92097 76353
units <- which(keep);
units6 <- units6[keep];
rm(keep);
# Import data
for (ee in 1:nbrOfEnzymes(ufl)) {
ufl[units,ee] <- ufl6[units6,ee];
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Update footer
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
footer <- readFooter(ufl);
srcFile <- list(
filename=getFilename(ufl6),
filesize=getFileSize(ufl6),
checksum=getChecksum(ufl6)
);
footer$srcFiles <- c(footer$srcFiles, list(srcFile=srcFile));
writeFooter(ufl, footer);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Statistics
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
print(ufl);
## AromaUflFile:
## Name: GenomeWideSNP_5
## Tags: Full,r2,na26,HB20080723
## Pathname: annotationData/chipTypes/GenomeWideSNP_5/GenomeWideSNP_5,Full,r2,na26,HB20080723.ufl
## File size: 3.51MB
## RAM: 0.00MB
## Number of data rows: 920928
## File format: v1
## Dimensions: 920928x2
## Column classes: integer, integer
## Number of bytes per column: 2, 2
## Footer: <platform>Affymetrix</platform><chipType>GenomeWideSNP_5,Full,r2</chipType><createdOn>20080723 16:09:57 PDT</createdOn><createdBy><fullname>Henrik Bengtsson</fullname><email>[...]</email></createdBy><srcFiles><srcFile><filename>GenomeWideSNP_5.na26.annot.csv</filename><filesize>755337946</filesize><checksum>af59235b6fccada7f871257149a89215</checksum></srcFile><srcFile><filename>GenomeWideSNP_5.na26.annot.csv</filename><filesize>755337946</filesize><checksum>af59235b6fccada7f871257149a89215</checksum></srcFile><srcFile><filename>GenomeWideSNP_5.na26.annot.csv</filename><filesize>755337946</filesize><checksum>af59235b6fccada7f871257149a89215</checksum></srcFile></srcFiles>
## Chip type: GenomeWideSNP_5,Full,r2
## Platform: Affymetrix
print(getChecksum(ufl));
## [1] "9d73f5a7689cac14c331ab661cf50ea9"
x <- summaryOfUnits(ufl, enzymes=c("NspI", "StyI"));
print(x);
## GenomeWideSNP_5,Full,na26+,HB20080723:
## snp cnp affxSnp other total
## enzyme1-only 102627 140099 0 0 242726
## enzyme2-only 90353 1208 0 0 91561
## both 249553 171077 0 0 420630
## missing 58035 104885 3022 69 166011
## total 500568 417269 3022 69 920928
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.