Nothing
## ----style, eval=TRUE, echo=FALSE, results='asis'--------------------------
BiocStyle::latex()
## ----include=FALSE---------------------------------------------------------
library(knitr)
opts_chunk$set(tidy=FALSE)
## ----<available schemas, results='hide'------------------------------------
library(DBI)
library(org.Hs.eg.db)
library(AnnotationForge)
available.dbschemas()
## ----setup0, results='hide', echo=FALSE-------------------------------
options(continue=" ", prompt="R> ", width=72L)
## ----setup, results='hide'--------------------------------------------
library(hgu95av2.db)
## ----objects----------------------------------------------------------
ls("package:hgu95av2.db")
## ----Question #1, echo=FALSE, results='hide'--------------------------
library(hgu95av2.db)
search()
hgu95av2_dbschema()
org.Hs.eg_dbschema()
## ----QAlisting--------------------------------------------------------
qcdata = capture.output(hgu95av2())
head(qcdata, 20)
## ----mapcounts, eval=FALSE--------------------------------------------
# hgu95av2MAPCOUNTS
## ----envApiDemo1------------------------------------------------------
all_probes <- ls(hgu95av2ENTREZID)
length(all_probes)
set.seed(0xa1beef)
probes <- sample(all_probes, 5)
probes
## ----envApiDemo2------------------------------------------------------
hgu95av2ENTREZID[[probes[1]]]
hgu95av2ENTREZID$"31882_at"
syms <- unlist(mget(probes, hgu95av2SYMBOL))
syms
## ----helpDemo, eval= FALSE, results='hide'----------------------------
# ?hgu95av2CHRLOC
## ----Question #2, echo=FALSE, results='hide'--------------------------
mget(probes, hgu95av2CHRLOC, ifnotfound=NA)[1:2]
## ----as.list, eval=FALSE----------------------------------------------
# system.time(as.list(hgu95av2SYMBOL)[1:10])
#
# ## vs:
#
# system.time(as.list(hgu95av2SYMBOL[1:10]))
## ----show.revmap------------------------------------------------------
unlist(mget(syms, revmap(hgu95av2SYMBOL)))
## ----thisworks--------------------------------------------------------
as.list(revmap(hgu95av2PATH)["00300"])
## ----revmap2----------------------------------------------------------
x <- hgu95av2PATH
## except for the name, this is exactly revmap(x)
revx <- hgu95av2PATH2PROBE
revx2 <- revmap(x, objName="PATH2PROBE")
revx2
identical(revx, revx2)
as.list(revx["00300"])
## ----revmap2b---------------------------------------------------------
Term("GO:0000018")
Definition("GO:0000018")
## ----Question #3, echo=FALSE, results='hide'--------------------------
rs = ls(revmap(org.Hs.egREFSEQ))[4:6]
EGs = mget(rs, revmap(org.Hs.egREFSEQ), ifnotfound=NA)
##Then get the GO terms.
GOs = mget(unlist(EGs), org.Hs.egGO, ifnotfound=NA)
GOs
##Extract the GOIDs from this list:
GOIDs = as.character(unique(sapply(GOs, names)))
##Then look up what these terms are:
Term(GOIDs)
## ----toTable----------------------------------------------------------
head(toTable(hgu95av2GO[probes]))
## ----undirectedMethod-------------------------------------------------
toTable(x)[1:6, ]
toTable(revx)[1:6, ]
## ----directedMethods--------------------------------------------------
length(x)
length(revx)
allProbeSetIds <- keys(x)
allKEGGIds <- keys(revx)
## ----moreUndirectedMethods--------------------------------------------
junk <- Lkeys(x) # same for all maps in hgu95av2.db (except pseudo-map
# MAPCOUNTS)
Llength(x) # nb of Lkeys
junk <- Rkeys(x) # KEGG ids for PATH/PATH2PROBE maps, GO ids for
# GO/GO2PROBE/GO2ALLPROBES maps, etc...
Rlength(x) # nb of Rkeys
## ----moreKeysMethods--------------------------------------------------
x = hgu95av2ENTREZID[1:10]
## Directed methods
mappedkeys(x) # mapped keys
count.mappedkeys(x) # nb of mapped keys
## Undirected methods
mappedLkeys(x) # mapped left keys
count.mappedLkeys(x) # nb of mapped Lkeys
## ----isNA-------------------------------------------------------------
y = hgu95av2ENTREZID[isNA(hgu95av2ENTREZID)] # usage like is.na()
Lkeys(y)[1:4]
## ----Question #4, echo=FALSE, results='hide'--------------------------
count.mappedLkeys(hgu95av2GO)
Llength(hgu95av2GO) - count.mappedLkeys(hgu95av2GO)
mappedLkeys(hgu95av2GO)[1]
toTable(hgu95av2GO["1000_at"])
## ----revmapUseCases---------------------------------------------------
x <- hgu95av2CHR
Rkeys(x)
chroms <- Rkeys(x)[23:24]
chroms
Rkeys(x) <- chroms
toTable(x)
## ----easy-------------------------------------------------------------
z <- as.list(revmap(x)[chroms])
names(z)
z[["Y"]]
## ----evilUnlist-------------------------------------------------------
chrs = c("12","6")
mget(chrs, revmap(hgu95av2CHR[1:30]), ifnotfound=NA)
## ----evilUnlist2------------------------------------------------------
unlist(mget(chrs, revmap(hgu95av2CHR[1:30]), ifnotfound=NA))
## ----evilUnlist3------------------------------------------------------
unlist2(mget(chrs, revmap(hgu95av2CHR[1:30]), ifnotfound=NA))
## ----cytogenetic2-----------------------------------------------------
x <- hgu95av2MAP
pbids <- c("38912_at", "41654_at", "907_at", "2053_at", "2054_g_at",
"40781_at")
x <- subset(x, Lkeys=pbids, Rkeys="18q11.2")
toTable(x)
## ----coerce-----------------------------------------------------------
pb2cyto <- as.character(x)
pb2cyto[pbids]
## ----coercWarnings----------------------------------------------------
cyto2pb <- as.character(revmap(x))
## ----multiProbes------------------------------------------------------
## How many probes?
dim(hgu95av2ENTREZID)
## Make a mapping with multiple probes exposed
multi <- toggleProbes(hgu95av2ENTREZID, "all")
## How many probes?
dim(multi)
## ----multiProbes2-----------------------------------------------------
## Make a mapping with ONLY multiple probes exposed
multiOnly <- toggleProbes(multi, "multiple")
## How many probes?
dim(multiOnly)
## Then make a mapping with ONLY single mapping probes
singleOnly <- toggleProbes(multiOnly, "single")
## How many probes?
dim(singleOnly)
## ----multiProbes3-----------------------------------------------------
## Test the multiOnly mapping
hasMultiProbes(multiOnly)
hasSingleProbes(multiOnly)
## Test the singleOnly mapping
hasMultiProbes(singleOnly)
hasSingleProbes(singleOnly)
## ----orgSchema, results='hide'----------------------------------------
org.Hs.eg_dbschema()
## ----connObj, results='hide'------------------------------------------
org.Hs.eg_dbconn()
## ----connObj2, results='hide'-----------------------------------------
query <- "SELECT gene_id FROM genes LIMIT 10;"
result = dbGetQuery(org.Hs.eg_dbconn(), query)
result
## ----Question #5, echo=FALSE, results='hide'--------------------------
sql <- "SELECT gene_id, chromosome FROM genes AS g, chromosomes AS c WHERE g._id=c._id;"
dbGetQuery(org.Hs.eg_dbconn(),sql)[1:10,]
##OR
toTable(org.Hs.egCHR)[1:10,]
## ----complexEnv, eval=FALSE-------------------------------------------
# ## Obtain SYMBOLS with at least one GO BP
# ## annotation with evidence IMP, IGI, IPI, or IDA.
# system.time({
# bpids <- eapply(hgu95av2GO, function(x) {
# if (length(x) == 1 && is.na(x))
# NA
# else {
# sapply(x, function(z) {
# if (z$Ontology == "BP")
# z$GOID
# else
# NA
# })
# }
# })
# bpids <- unlist(bpids)
# bpids <- unique(bpids[!is.na(bpids)])
# g2p <- mget(bpids, hgu95av2GO2PROBE)
# wantedp <- lapply(g2p, function(x) {
# x[names(x) %in% c("IMP", "IGI", "IPI", "IDA")]
# })
# wantedp <- wantedp[sapply(wantedp, length) > 0]
# wantedp <- unique(unlist(wantedp))
# ans <- unlist(mget(wantedp, hgu95av2SYMBOL))
# })
# length(ans)
# ans[1:10]
## ----schema, results='hide'-------------------------------------------
hgu95av2_dbschema()
## ----schema2, results='hide'------------------------------------------
hgu95av2ORGPKG
## ----schema3, results='hide'------------------------------------------
org.Hs.eg_dbschema()
## ----hgu95av2_org_join, tidy=FALSE------------------------------------
orgDBLoc = system.file("extdata", "org.Hs.eg.sqlite", package="org.Hs.eg.db")
attachSQL = paste("ATTACH '", orgDBLoc, "' AS orgDB;", sep = "")
dbGetQuery(hgu95av2_dbconn(), attachSQL)
## ----complexDb--------------------------------------------------------
system.time({
SQL <- "SELECT DISTINCT probe_id,symbol FROM probes, orgDB.gene_info AS gi, orgDB.genes AS g, orgDB.go_bp AS bp WHERE bp._id=g._id AND gi._id=g._id AND probes.gene_id=g.gene_id AND bp.evidence IN ('IPI', 'IDA', 'IMP', 'IGI')"
zz <- dbGetQuery(hgu95av2_dbconn(), SQL)
})
#its a good idea to always DETACH your database when you are finished...
dbGetQuery(hgu95av2_dbconn(), "DETACH orgDB" )
## ----Question #6, echo=FALSE, results='hide'--------------------------
sql <- "SELECT gene_id, start_location, end_location, cytogenetic_location FROM genes AS g, chromosome_locations AS c, cytogenetic_locations AS cy WHERE g._id=c._id AND g._id=cy._id"
dbGetQuery(org.Hs.eg_dbconn(),sql)[1:10,]
## ----Question #7, echo=FALSE, results='hide'--------------------------
orgDBLoc = system.file("extdata", "org.Hs.eg.sqlite", package="org.Hs.eg.db")
attachSQL = paste("ATTACH '", orgDBLoc, "' AS orgDB;", sep = "")
dbGetQuery(hgu95av2_dbconn(), attachSQL)
goDBLoc = system.file("extdata", "GO.sqlite", package="GO.db")
attachSQL = paste("ATTACH '", goDBLoc, "' AS goDB;", sep = "")
dbGetQuery(hgu95av2_dbconn(), attachSQL)
SQL <- "SELECT DISTINCT p.probe_id, gi.symbol, gt.go_id, gt.definition
FROM probes
AS p, orgDB.gene_info AS gi, orgDB.genes AS g, orgDB.go_bp
AS bp, goDB.go_term AS gt
WHERE bp._id=g._id AND gi._id=g._id AND p.gene_id=g.gene_id
AND bp.evidence IN ('IPI', 'IDA', 'IMP', 'IGI') AND gt.go_id=bp.go_id"
zz <- dbGetQuery(hgu95av2_dbconn(), SQL)
dbGetQuery(hgu95av2_dbconn(), "DETACH orgDB")
dbGetQuery(hgu95av2_dbconn(), "DETACH goDB")
## ----SessionInfo, echo=FALSE------------------------------------------
sessionInfo()
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