Nothing
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Data sources
#https://www.affymetrix.com/estore/browse/products.jsp?productId=131533
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (interactive()) savehistory();
library("aroma.affymetrix");
library("R.menu");
verbose <- Verbose(threshold=-10, timestamp=TRUE);
options(width=60);
chipType <- "GenomeWideSNP_6";
cdfTags <- "Full";
nbrOfEnzymes <- 2;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# User settings
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
## setOption(aromaSettings, "user/initials", "HB");
## setOption(aromaSettings, "user/fullname", "Henrik Bengtsson");
## obf <- sprintf("%s@%s", "henrik.bengtsson", "aroma-project.org");
## setOption(aromaSettings, "user/email", obf);
## saveAnywhere(aromaSettings);
fullname <- getOption(aromaSettings, "user/fullname");
stopifnot(!is.null(fullname));
email <- getOption(aromaSettings, "user/email");
stopifnot(!is.null(email));
user <- getOption(aromaSettings, "user/initials");
stopifnot(!is.null(user));
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Settings
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
naVersions <- 30:33;
naVersion <- textMenu(naVersions, title="Choose NetAffx version: ", value=TRUE);
datestamp <- format(Sys.Date(), format="%Y%m%d");
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup required annotation files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cdf <- AffymetrixCdfFile$byChipType(chipType, tags=cdfTags);
rm(csvList);
print(cdf);
csvList <- list();
tagsList <- c(
main=sprintf(".na%s", naVersion),
cn=sprintf(".cn.na%s", naVersion)
);
for (key in names(tagsList)) {
tags <- tagsList[[key]];
pathname <- AffymetrixNetAffxCsvFile$findByChipType(chipType, tags=tags);
if (isFile(pathname)) {
csvList[[key]] <- AffymetrixNetAffxCsvFile(pathname);
}
rm(tags);
}
print(csvList);
genomeVersion <- getHeaderAttributes(csvList[[1]])[["genome-version"]];
genomeVersion <- Arguments$getCharacter(genomeVersion, nchar=4, length=c(1,1));
dbSNPVersion <- getHeaderAttributes(csvList[[1]])[["dbSNP-version"]];
dbSNPVersion <- Arguments$getInteger(dbSNPVersion);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Import UFL from CSV files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
tags <- sprintf("na%s,%s,dbSNP%d,%s%s", naVersion, genomeVersion, dbSNPVersion, user, datestamp);
ufl <- NULL;
tryCatch({
ufl <- AromaUflFile$byChipType(getChipType(cdf), tags=tags);
}, error = function(ex) {})
if (is.null(ufl)) {
ufl <- AromaUflFile$allocateFromCdf(cdf, tags=tags, nbrOfEnzymes=nbrOfEnzymes);
}
print(ufl);
for (kk in seq_along(csvList)) {
csv <- csvList[[kk]];
print(csv);
units <- importFrom(ufl, csv, verbose=verbose);
str(units);
## GenomeWideSNP_6.na<XX>.annot.csv: int [1:934968] 334945 334944 ...
## GenomeWideSNP_6.cn.na<XX>.annot.csv: int [1:945826] 935622 935777 ...
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Update the file footer
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
srcFileTags <- list();
srcFiles <- c(list(cdf), csvList);
for (kk in seq_along(srcFiles)) {
srcFile <- srcFiles[[kk]];
tags <- list(
filename=getFilename(srcFile),
filesize=getFileSize(srcFile),
checksum=getChecksum(srcFile)
);
srcFileTags[[kk]] <- tags;
}
print(srcFileTags);
footer <- readFooter(ufl);
footer$createdBy <- list(
fullname = fullname,
email = email
);
names(srcFileTags) <- sprintf("srcFile%d", seq_along(srcFileTags));
footer$srcFiles <- srcFileTags;
writeFooter(ufl, footer);
print(ufl);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# WHAT'S NEW:
#
# o na32 -> na33
# - Back to no filtering? By comparing CSV content for a SNP,
# I've verified that the parsing is correct.
# o na31 -> na32
# - Are Affymetrix doing filter for us again?
# o na30 -> na31
# - Lots of differences; Affymetrix no longer filter for us.
# o na27.1 -> na30
# - No changes.
# o na27 -> na27.1
# - No changes.
# o na26 -> na27
# - No changes.
# o na24 -> na26
# - All changes are for SNP units.
# - There are 6 NspI and 14 StyI changes in SNP fragment lengths,
# which some are only minor.
# - There are 1108 more SNPs that now have missing values.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ufl <- AromaUflFile$byChipType("GenomeWideSNP_6,Full", tags="na33");
ufl0 <- AromaUflFile$byChipType("GenomeWideSNP_6,Full", tags="na32");
x <- summaryOfUnits(ufl);
x0 <- summaryOfUnits(ufl0);
print(x);
print(x0);
## GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140117
## snp cnp affxSnp other total
## enzyme1-only 0 445237 0 0 445237
## enzyme2-only 210 5 0 0 215
## both 929892 500368 3018 0 1433278
## missing 1844 216 4 621 2685
## total 931946 945826 3022 621 1881415
## GenomeWideSNP_6,Full,na32,hg19,dbSNP132,HB20140118
## snp cnp affxSnp other total
## enzyme1-only 242858 435414 777 0 679049
## enzyme2-only 158233 19259 620 0 178112
## both 528831 490937 1621 0 1021389
## missing 2024 216 4 621 2865
## total 931946 945826 3022 621 1881415
## GenomeWideSNP_6,na31,hg19,HB20110328.ufl
## snp cnp affxSnp other total
## enzyme1-only 577 9609 0 0 10186
## enzyme2-only 502 23432 0 0 23934
## both 929322 912574 0 0 1841896
## missing 1545 211 3022 621 5399
## total 931946 945826 3022 621 1881415
## GenomeWideSNP_6,na30,hg18,HB20100215.ufl
## snp cnp affxSnp other total
## enzyme1-only 246080 451191 0 0 697271
## enzyme2-only 160899 0 0 0 160899
## both 522472 494615 0 0 1017087
## missing 2495 20 3022 621 6158
## total 931946 945826 3022 621 1881415
## GenomeWideSNP_6,na27.1,hg??,HB20??????.ufl
## snp cnp affxSnp other total
## enzyme1-only 246080 451191 0 0 697271
## enzyme2-only 160899 0 0 0 160899
## both 522472 494615 0 0 1017087
## missing 2495 20 3022 621 6158
## total 931946 945826 3022 621 1881415
print(x-x0);
## snp cnp affxSnp other total
## enzyme1-only -242858 9823 -777 0 -233812
## enzyme2-only -158023 -19254 -620 0 -177897
## both 401061 9431 1397 0 411889
## missing -180 0 0 0 -180
## total 0 0 0 0 0
# Differences
for (cc in 1:nbrOfColumns(ufl)) {
units <- whichVector(ufl[,cc] != ufl0[,cc], na.rm=TRUE);
if (length(units) > 0) {
df <- cbind(units, ufl[units,cc], ufl0[units,cc],
ufl[units,cc]-ufl0[units,cc]);
colnames(df)[ncol(df)] <- "delta";
print(df);
}
}
## units length length delta
## 1 21988 1663 919 744
## 2 82781 445 177 268
## 3 87809 871 1259 -388
## 4 126538 1062 1994 -932
## ...
# Differences in NAs
for (cc in 1:nbrOfColumns(ufl)) {
units <- whichVector(is.na(ufl[,cc]) != is.na(ufl0[,cc]));
if (length(units) > 0) {
df <- cbind(units, ufl[units,cc], ufl0[units,cc]);
str(df);
}
}
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