Dear R-helpers & bioconductor
Sorry for cross-posting, this concerns R-programming stuff applied on
Bioconductor context.
Also sorry for this long message, I try to be complete in my request.
I am trying to write a subset method for a specific class (ExpressionSet
from Bioconductor) allowing selection more flexible than "[" method .
The schema I am thinking for is the following:
subset.ExpressionSet <- function(x,subset,...){
}
I will use the subset argument for rows (genes), as in default method.
Now I would like to allow to select different columns (features) based on
phenotypic data.
phenotypic data provides detailed information about the columns.
Basically, first function I have written allows the following:
> sub1 <- subset(ExpressionSetObject, subset=NULL, V1=value1, v2=value2)
# subset=NULL takes all rows
See: there are two conditions on two variables belonging to the associated
data.frame encapsulated in the ExpressionSetObject (to be complete, the
conditions will be applied on more of 2 columns, as they are used on the
phylogenic data.frame that concerns all variables)
To simplify a little bit, this would nearly return:
ExpressionSetObject[,V1==value & V2==value]
This is nice as I can already handle any number of conditions on variables
values thanks to '...'. First step is
conditions <- list(...) and are then handled later in code
Nevertheless, those conditions are basic (one value).
I would like to handle arbitrary conditions, such as: V1 %in% c(value1,
value2)
More simple expression would be passed with V2==value instead of V2=value2
My very problem is that I don't know how to turn '...' into an object
containing those conditions that could be used later.
My attempt which seems the nearest is:
> foo <- function(...){
> as.expression(substitute(list(...)))
> }
>foo(x==1,y%in%1:2)
expression(list(x == 1, y %in% 1:2))
where as I would like to have something like
list(expression(x==1), expression(y %in% 1:2))
those expressions beeing evaluated later on in the context of my specific
object.
Are there any existing function where '...' are already handled the way I
want so that I can mimic?
Thanks for any insight.
Eric
---
For those who have Biobase available, here is my current subset function and
a demo-case that explains a little bit.
library(Biobase)
example(ExpressionSet) # create sample object
print(expressionSet)
# now my subset function as it is
subset.ExpressionSet <- function(x,subset=NULL,verbose=TRUE,...){
# subset is used to subset on rows
# ... is used to make multiple conditions on columns based on pData
# list of conditions is handled in ...
stopifnot(is(x,"ExpressionSet"))
phenoData <- pData(x)
listCriteria <- list(...)
if (is.null(subset)) subset <- rep(TRUE,nrow(exprs(x)))
subset <- subset & !is.na(subset)
retainedCriteria <- list()
tmp <- sapply(names(listCriteria), function(critname) {
if(!critname %in% colnames(phenoData)){
if (verbose) cat("\n*** subsetCompounds: Dropped
criteria:",critname, "not in phenoData of object\n")
}else{
if(is.null(listCriteria[critname])) listCriteria[[critname]]<-
unique(phenoData[,critname])
retainedCriteria[[critname]] <<- phenoData[,critname] %in%
listCriteria[critname]
}
})
criteriaValues <- do.call("cbind",retainedCriteria)
selectedColumns <- rownames(phenoData)[apply(criteriaValues,1,logic)]
## cbind(phenoData,criteriaValues)
out <- x[subset,selectedColumns]
if (verbose) cat('\n',length(selectedColumns),' columns selected
(',paste(selectedColumns,collapse=' '),
')\n',sep='')
invisible(return(out))
}
# looking at phenotypic data associated with the sample expressionSet
> pData(expressionSet)
sex type score
A Female Control 0.75
B Male Case 0.40
C Male Control 0.73
D Male Case 0.42
E Female Case 0.93
F Male Control 0.22
G Male Case 0.96
H Male Case 0.79
I Female Case 0.37
J Male Control 0.63
K Male Case 0.26
L Female Control 0.36
M Male Case 0.41
N Male Case 0.80
O Female Case 0.10
P Female Control 0.41
Q Female Case 0.16
R Male Control 0.72
S Male Case 0.17
T Female Case 0.74
U Male Control 0.35
V Female Control 0.77
W Male Control 0.27
X Male Control 0.98
Y Female Case 0.94
Z Female Case 0.32
# now the sample use
> (subset1 =subset(expressionSet,sex="Male",type="Control"))
7 columns selected (C F J R U W X)
ExpressionSet (storageMode: lockedEnvironment)
assayData: 500 features, 7 samples
element names: exprs, se.exprs
phenoData
sampleNames: C, F, ..., X (7 total)
varLabels and varMetadata description:
sex: Female/Male
type: Case/Control
score: Testing Score
featureData
featureNames: AFFX-MurIL2_at, AFFX-MurIL10_at, ..., 31739_at (500 total)
fvarLabels and fvarMetadata description: none
experimentData: use 'experimentData(object)'
Annotation: hgu95av2
# what I would like to allow in use:
(subset2 = subset(expressionSet, sex=="Male", score > 0.75) # note the ==
instead of =
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