## Chunk 1
|
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library("hgu95av2")
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## Chunk 2
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byChr = split(names(chrVec), chrVec)
|
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## Chunk 3
|
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byChr[["Y"]]
|
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## Chunk 4
|
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library("hgu95av2")
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## Chunk 5
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myPos = eapply(hgu95av2MAP, function(x) grep("^17p", x, value=TRUE))
|
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## Chunk 6
|
|||
myFindMap = function(mapEnv, which) {
|
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## Chunk 7
|
|||
x = matrix(1:6, nc=2, dimnames=list(letters[1:3], LETTERS[1:2]))
|
|||
## Chunk 8
|
|||
s1 = list(a=1:3,b= 11:12,c= letters[1:6])
|
|||
## Chunk 9
|
|||
mapP = as.list(hgu95av2MAP)
|
|||
## Chunk 10
|
|||
mlt = table(mLens)
|
|||
## Chunk 11
|
|||
len3 = mLens[mLens==3]
|
|||
## Chunk 12
|
|||
len2 = names(mLens[mLens==2])
|
|||
## Chunk 13
|
|||
missingMap = unlist(eapply(hgu95av2MAP,
|
|||
## Chunk 14
|
|||
mapPs = sapply(mapP, function(x) x[1])
|
|||
## Chunk 15
|
|||
library("RSQLite")
|
|||
## Chunk 16
|
|||
rs = dbSendQuery(con, "select * from USArrests")
|
|||
## Chunk 17
|
|||
dbListTables(con)
|
|||
## Chunk 18
|
|||
query = paste("SELECT name FROM sqlite_master WHERE",
|
|||
## Chunk 19
|
|||
rs = dbSendQuery(con,
|
|||
## Chunk 20
|
|||
unlink("test")
|
|||
## Chunk 21
|
|||
library("RSQLite")
|
|||
## Chunk 22
|
|||
query = paste("SELECT go_ont.go_id, go_ont.ont,",
|
|||
|
|||
## Chunk 24
|
|||
query = paste("SELECT g1.*, g2.evi FROM go_probe g1,",
|
|||
## Chunk 25
|
|||
library("hgu95av2.db")
|
|||
## Chunk 26
|
|||
colnames(hgu95av2GO)
|
|||
## Chunk 27
|
|||
links(hgu95av2GO)[1:10,]
|
|||
## Chunk 28
|
|||
is(hgu95av2SYMBOL, "Bimap")
|
|||
## Chunk 29
|
|||
myl=list(a="w", b="x", c="y")
|
|||
## Chunk 30
|
|||
queryAlias = function(x) {
|
|||
## Chunk 31
|
|||
findEGs(mycon, c("ALL1", "AF4", "BCR", "ABL"))
|
|||
## Chunk 32
|
|||
GOdbloc = system.file("extdata", "GO.sqlite", package="GO.db")
|
|||
## Chunk 33
|
|||
sql = paste("SELECT DISTINCT a.go_id AS 'hgu95av2.go_id',",
|
|||
## Chunk 34
|
|||
## schema = capture.output(hgu95av2_dbschema())
|
|||
## Chunk 35
|
|||
qcdata = capture.output(hgu95av2())
|
|||
## Chunk 36
|
|||
## hgu95av2MAPCOUNTS
|
|||
## Chunk 37
|
|||
tryCatch(library("human.db0"), error=function(e) {
|
|||
## Chunk 38
|
|||
## source("http://bioconductor.org/biocLite.R")
|
|||
## Chunk 39
|
|||
hgu95av2_IDs = system.file("extdata",
|
|||
## Chunk 40
|
|||
tmpout = tempdir()
|
|||
## Chunk 41
|
|||
seed <- new("AnnDbPkgSeed",
|
|||
## Chunk 42
|
|||
makeHUMANCHIP_DB(affy=FALSE,
|
|||
## Chunk 43
|
|||
Yeastfn = system.file("extdata", "yeast_small-01.xml", package="RBioinf")
|
|||
## Chunk 44
|
|||
yeastIntAct = xmlTreeParse(Yeastfn)
|
|||
|
|||
## Chunk 46
|
|||
nullf = function(x, ...) NULL
|
|||
## Chunk 47
|
|||
object.size(yeastIntAct)
|
|||
## Chunk 48
|
|||
yeast3 = xmlTreeParse(Yeastfn, useInternalNodes=TRUE)
|
|||
## Chunk 49
|
|||
iaM = getNodeSet(yeast3,
|
|||
## Chunk 50
|
|||
interactors = getNodeSet(yeast3,
|
|||
## Chunk 51
|
|||
interactors = xpathApply(yeast3,
|
|||
## Chunk 52
|
|||
entSH = function(name, attrs, ...) {
|
|||
## Chunk 53
|
|||
hOrg = function(name, attrs, ...) {
|
|||
## Chunk 54
|
|||
s1 = xmlEventParse(Yeastfn,
|
|||
## Chunk 55
|
|||
url = paste("http://www.bioconductor.org/checkResults/",
|
|||
## Chunk 56
|
|||
f1 = getNodeSet(s1, "//a[@href]")
|
|||
## Chunk 57
|
|||
f2 = getNodeSet(s1, "//b/a[@href]")
|
|||
## Chunk 58
|
|||
pkgs = sapply(f1, xmlGetAttr, "href")
|
|||
## Chunk 59
|
|||
ezURL = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
|
|||
## Chunk 60
|
|||
library("biomaRt")
|
|||
## Chunk 61
|
|||
ensM = useMart("ensembl")
|
|||
## Chunk 62
|
|||
## ensMH = useMart("ensembl",
|
|||
## Chunk 63
|
|||
filterSummary(ensMH)
|
|||
## Chunk 64
|
|||
head(attributeSummary(ensMH))
|
|||
## Chunk 65
|
|||
entrezID = c("983", "3581", "1017")
|
|||
## Chunk 66
|
|||
ensembl = useMart("ensembl",
|
|||
## Chunk 67
|
|||
library(GEOquery)
|
|||
## Chunk 68
|
|||
## s1 = experimentData(eset)
|
|||
## Chunk 69
|
|||
library("KEGG")
|
|||
## Chunk 70
|
|||
SA = gsub("^sce:", "", SoapAns)
|
|||