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## ----style, echo = FALSE, results = 'asis', message=FALSE------------------
BiocStyle::markdown()
## ----supportedFilters------------------------------------------------------
library(AnnotationFilter)
supportedFilters()
## ----symbol-filter---------------------------------------------------------
library(AnnotationFilter)
smbl <- SymbolFilter("BCL2")
smbl
## ----symbol-startsWith-----------------------------------------------------
smbl <- SymbolFilter("BCL2", condition = "startsWith")
smbl
## ----convert-expression----------------------------------------------------
smbl <- AnnotationFilter(~ symbol == "BCL2")
smbl
## ----convert-multi-expression----------------------------------------------
flt <- AnnotationFilter(~ symbol == "BCL2" &
tx_biotype == "protein_coding")
flt
## ----nested-query----------------------------------------------------------
## Define the filter query for the first pair of filters.
afl1 <- AnnotationFilterList(SymbolFilter("BCL2L11"),
TxBiotypeFilter("nonsense_mediated_decay"))
## Define the second filter pair in ( brackets should be combined.
afl2 <- AnnotationFilterList(SymbolFilter("BCL2"),
TxBiotypeFilter("protein_coding"))
## Now combine both with a logical OR
afl <- AnnotationFilterList(afl1, afl2, logicOp = "|")
afl
## ----define-data.frame-----------------------------------------------------
## Define a simple gene table
gene <- data.frame(gene_id = 1:10,
symbol = c(letters[1:9], "b"),
seq_name = paste0("chr", c(1, 4, 4, 8, 1, 2, 5, 3, "X", 4)),
stringsAsFactors = FALSE)
gene
## ----simple-symbol---------------------------------------------------------
smbl <- SymbolFilter("b")
## ----simple-symbol-condition-----------------------------------------------
condition(smbl)
## ----simple-symbol-value---------------------------------------------------
value(smbl)
## ----simple-symbol-field---------------------------------------------------
field(smbl)
## ----doMatch---------------------------------------------------------------
doMatch <- function(x, filter) {
do.call(condition(filter), list(x[, field(filter)], value(filter)))
}
## Apply this function
doMatch(gene, smbl)
## ----doExtract-------------------------------------------------------------
doExtract <- function(x, filter) {
x[doMatch(x, filter), ]
}
## Apply it on the data
doExtract(gene, smbl)
## ----doMatch-formula-------------------------------------------------------
doMatch <- function(x, filter) {
if (is(filter, "formula"))
filter <- AnnotationFilter(filter)
do.call(condition(filter), list(x[, field(filter)], value(filter)))
}
doExtract(gene, ~ gene_id == '2')
## ----orgDb, message = FALSE------------------------------------------------
## Load the required packages
library(org.Hs.eg.db)
library(RSQLite)
## Get the database connection
dbcon <- org.Hs.eg_dbconn()
## What tables do we have?
dbListTables(dbcon)
## ----gene_info-------------------------------------------------------------
## What fields are there in the gene_info table?
dbListFields(dbcon, "gene_info")
## ----doExtractSQL----------------------------------------------------------
doExtractGene <- function(x, filter) {
gene <- dbGetQuery(x, "select * from gene_info")
doExtract(gene, filter)
}
## Extract all entries for BCL2
bcl2 <- doExtractGene(dbcon, SymbolFilter("BCL2"))
bcl2
## ----simpleSQL-------------------------------------------------------------
## Define a simple function that covers some condition conversion
conditionForSQL <- function(x) {
switch(x,
"==" = "=",
x)
}
## Define a function to translate a filter into an SQL where condition.
## Character values have to be quoted.
where <- function(x) {
if (is(x, "CharacterFilter"))
value <- paste0("'", value(x), "'")
else value <- value(x)
paste0(field(x), conditionForSQL(condition(x)), value)
}
## Now "translate" a filter using this function
where(SeqNameFilter("Y"))
## ----doExtractGene2--------------------------------------------------------
## Define a function that
doExtractGene2 <- function(x, filter) {
if (is(filter, "formula"))
filter <- AnnotationFilter(filter)
query <- paste0("select * from gene_info where ", where(filter))
dbGetQuery(x, query)
}
bcl2 <- doExtractGene2(dbcon, ~ symbol == "BCL2")
bcl2
## ----performance-----------------------------------------------------------
system.time(doExtractGene(dbcon, ~ symbol == "BCL2"))
system.time(doExtractGene2(dbcon, ~ symbol == "BCL2"))
## ----symbol-overwrite------------------------------------------------------
## Default method from AnnotationFilter:
field(SymbolFilter("a"))
## Overwrite the default method.
setMethod("field", "SymbolFilter", function(object, ...) "hgnc_symbol")
## Call to field returns now the "correct" database column
field(SymbolFilter("a"))
## ----si--------------------------------------------------------------------
sessionInfo()
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