/usr/lib/R/site-library/AnnotationFilter/doc/AnnotationFilter.R is in r-bioc-annotationfilter 1.2.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 | ## ----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"))
## ----si--------------------------------------------------------------------
sessionInfo()
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