[BioC] conditional replace column values with values from a different column

[Hervé Pagès]

Hi Assa, Wolfgang,

On 11-04-08 01:06 AM, Wolfgang Huber wrote:
> Hi Assa
>
> bp_subset$Term = with(bp_subset, ifelse(is.na(Term), Term2, Term))
>
> The 'with' is tangential and could be omitted if you prefer to spell out
> the 'bp_subset$' three times.

Or slightly faster:

   idx <- which(is.na(bp_subset$Term))
   bp_subset$Term[idx] <- bp_subset$Term2[idx]

H.

>
> Wolfgang
>
> Il Apr/8/11 9:48 AM, Assa Yeroslaviz ha scritto:
>> Hi R Users,
>>
>> I have a data.frame with various NAs (df name is 'bp_subset'):
>> GOBPIDPvalueTermPvalue2Term2 1GO:00000414.991241e-03transition metal ion
>> transport0.0305047593transition metal ion transport 2GO:0000103NANA
>> 0.0475575125sulfate assimilation 3GO:0000904NANA0.0211635899cell
>> morphogenesis involved in differentiation
>> 4GO:0001505NANA0.0314384424regulation
>> of neurotransmitter levels 5GO:0001508NANA0.0017933627regulation of
>> action
>> potential 6GO:00016594.018995e-02temperature homeostasisNANA
>> I would like tobe abale to replace the 'NA' values of the column "Term",
>> with the values of column "Term2" (if they are not 'NA')
>> I tried to do it with an if statement, but it doesn't work correctly.
>>
>>> if (is.na(bp_subset[,3]))
>> bp_subset[,3]<- bp_subset[,5]Warning message:In if
>> (is.na(bp_subset[, 3])) bp_subset[, 3]<- bp_subset[, 5] :
>> the condition has length> 1 and only the first element will be used
>>
>> I also tried to do something like:
>>
>> bp_subset_test[is.na(bp_subset_test$Term)]<- bp_subset_test$Term2
>> Error in `[<-.data.frame`(`*tmp*`, is.na(bp_subset_test$Term), value =
>> c("transition metal ion transport", :
>> duplicate subscripts for columns
>>
>>
>> Is there another way of doing it?
>>
>> THX,
>>
>> Assa
>>
>>
>>> sessionInfo()R version 2.12.2 (2011-02-25)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] splines grid stats graphics grDevices utils
>> datasets methods base
>>
>> other attached packages:
>> [1] GSEABase_1.12.1 org.Mm.eg.db_2.4.6 Heatplus_1.20.0
>> ggplot2_0.8.9 proto_0.3-9.1
>> [6] reshape_0.8.4 plyr_1.4 gplots_2.8.0
>> caTools_1.11 bitops_1.0-4.1
>> [11] gdata_2.8.1 gtools_2.6.2 siggenes_1.24.0
>> multtest_2.7.1 Rgraphviz_1.29.0
>> [16] xtable_1.5-6 annotate_1.28.1 GO.db_2.4.5
>> biomaRt_2.6.0 GOstats_2.16.0
>> [21] RSQLite_0.9-4 DBI_0.2-5 graph_1.28.0
>> Category_2.16.0 AnnotationDbi_1.12.0
>> [26] Biobase_2.10.0
>>
>> loaded via a namespace (and not attached):
>> [1] MASS_7.3-11 RBGL_1.26.0 RCurl_1.5-0 XML_3.2-0
>> genefilter_1.32.0 survival_2.36-5
>> [7] tools_2.12.2
>>
>> [[alternative HTML version deleted]]
>>
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>


-- 
Hervé Pagès

Program in Computational Biology
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