PrettyOutput.R

Code snipits and programs written in R, S or S-PLUS library("annotate") data(eset) igenes <- geneNames(eset)[246:260]

gb <- scan(what=character(0)) "M57423" "Z70218" "L17328" "S81916" "U63332" "M77235" "X98175" "AB019392" "J03071" "D25272" "D63789" "D63789" "U19142" "U19147" "X16863" ""

ll <- scan(what=character(0)) "221823" "4330" "9637" "---" "---" "6331" "841" "27335" "---" "---" "6375" "---" "2543" "2578" "2215" ""

ug <- scan(what=character(0)) "Hs.169284 // ---" "Hs.268515 // full length" "Hs.103419 // full length" "Hs.380429 // ---" "--- // ---" "Hs.169331 // full length" "Hs.381231 // full length" "Hs.283781 // full length" "--- // ---" "--- // ---" "Hs.3195 // full length" "--- // ---" "Hs.176660 // full length" "Hs.272484 // full length" "Hs.372679 // full length" ""

ug <- sub(" //.*$", "", ug) ug

sp <- scan(what=character(0))

"P21108" "Q10571" "Q9UHY8" "Q16444" "---" "Q14524 /// Q8IZC9 /// Q8WTQ6 /// Q8WWN5 /// Q96J69" "Q14790" "Q9UBQ5" "---" "---" "P47992" "---" "Q13065 /// Q8IYC5" "Q13070" "O75015" ""

sp <- strsplit(sub("---", " ", as.character(sp)), "///")

dat <- exprs(eset)[igenes, 1:10] FC <- rowMeans(dat[igenes, 1:5]) - rowMeans(dat[igenes, 6:10]) pval <- esApply(eset[igenes, 1:10], 1, function(x) t.test(x[1:5], x[6:10])$p.value) tstat <- esApply(eset[igenes, 1:10], 1, function(x) t.test(x[1:5], x[6:10])$statistic)

FC <- rowMeans(dat[igenes, 1:5]) - rowMeans(dat[igenes, 6:10]) pval <- esApply(eset[igenes, 1:10], 1, function(x) t.test(x[1:5], x[6:10])$p.value) tstat <- esApply(eset[igenes, 1:10], 1, function(x) t.test(x[1:5], x[6:10])$statistic)

name <- scan(what=character(0)) "hypothetical protein LOC221823" "meningioma (disrupted in balanced translocation) 1" "fasciculation and elongation protein zeta 2 (zygin II)" "Phosphoglycerate kinase {alternatively spliced}" "---" "sodium channel, voltage-gated, type V, alpha polypeptide" "caspase 8, apoptosis-related cysteine protease" "muscle specific gene" "---" "---" "chemokine (C motif) ligand 1" "---" "G antigen 1" "G antigen 6" "Fc fragment of IgG, low affinity IIIb, receptor for (CD16)" ""

name <- gsub("---", " ", name) name

genelist <- list(igenes, ug, ll, gb, sp) filename <- "Interesting_genes.html" title <- "An Artificial Set of Interesting Genes" othernames <- list(name, round(tstat, 2), round(pval, 3), round(FC, 1), round(dat, 2)) head <- c("Probe ID", "UniGene", "LocusLink", "GenBank", "SwissProt", "Gene Name", "t-statistic", "p-value", "Fold Change", "Sample 1", "Sample 2", "Sample 3", "Sample 4", "Sample 5", "Sample 6", "Sample 7", "Sample 8", "Sample 9", "Sample 10") repository <- list("affy", "ug", "ll", "gb", "sp") htmlpage(genelist, filename, title, othernames, head, repository = repository)

sessionInfo()