[R] remove rows based on row mean

[Adrian Johnson]

Wow. This is much cleaner and smarter than the for loop, cbind
thanks a lot .

On Thu, Aug 18, 2016 at 6:28 PM, Jim Lemon <drjimlemon at gmail.com> wrote:
> Hi Adrian,
> Try this:
>
> sm$rowmeans<-rowMeans(sm[,2:length(sm)])
> sm<-sm[order(sm$Gene,sm$rowmeans,decreasing=TRUE),]
> sm[-which(duplicated(sm$Gene)),]
>
> Jim
>
>
> On Fri, Aug 19, 2016 at 7:33 AM, Adrian Johnson
> <oriolebaltimore at gmail.com> wrote:
>> Hi Group,
>> I have a data matrix sm (dput code given below).
>>
>> I want to create a data matrix with rows with same variable that have
>> higher mean.
>>
>>> sm
>>      Gene GSM529305 GSM529306 GSM529307 GSM529308
>> 1    A1BG      6.57      6.72      6.83      6.69
>> 2    A1CF      2.91      2.80      3.08      3.00
>> 3   A2LD1      5.82      7.01      6.62      6.87
>> 4     A2M      9.21      9.35      9.32      9.19
>> 5     A2M      2.94      2.50      3.16      2.76
>> 6  A4GALT      6.86      5.75      6.06      7.04
>> 7   A4GNT      3.97      3.56      4.22      3.88
>> 8    AAA1      3.39      2.90      3.16      3.23
>> 9    AAAS      8.26      8.63      8.40      8.70
>> 10   AAAS      6.82      7.15      7.33      6.51
>>
>> For example in rows 4 and 5 have same variable Gene A2M. I want to
>> select only row that has higher mean. I wrote the following code that
>> gives me duplicate rows with higher mean but I cannot properly write
>> the result. Could someone help.  Thanks
>>
>> ugns <- unique(sm$Gene)
>>
>> exwidh = c()
>>
>> for(i in 1:length(ugns)){
>> k = ugns[i]
>> exwidh[i] <- sm[names(sort(rowMeans(sm[which(sm[,1]==k),2:ncol(sm)]),decreasing=TRUE)[1]),]
>> }
>>
>>
>>
>>
>>
>> structure(list(Gene = c("A1BG", "A1CF", "A2LD1", "A2M", "A2M",
>> "A4GALT", "A4GNT", "AAA1", "AAAS", "AAAS"), GSM529305 = c(6.57,
>> 2.91, 5.82, 9.21, 2.94, 6.86, 3.97, 3.39, 8.26, 6.82), GSM529306 = c(6.72,
>> 2.8, 7.01, 9.35, 2.5, 5.75, 3.56, 2.9, 8.63, 7.15), GSM529307 = c(6.83,
>> 3.08, 6.62, 9.32, 3.16, 6.06, 4.22, 3.16, 8.4, 7.33), GSM529308 = c(6.69,
>> 3, 6.87, 9.19, 2.76, 7.04, 3.88, 3.23, 8.7, 6.51)), .Names = c("Gene",
>> "GSM529305", "GSM529306", "GSM529307", "GSM529308"), row.names = c(NA,
>> 10L), class = "data.frame")
>>
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