[R] remove rows based on row mean

[jeremiah rounds]

library(data.table)
setDT(dt)
op = function(s){
mean0 = apply(s, 1, mean)
ret = s[which.max(mean0)]
ret$mean = mean0
ret
}
max_row = dt[, op(.SD), by = "Gene"]

Thanks,
Jeremiah

On Thu, Aug 18, 2016 at 2:33 PM, 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")
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

	[[alternative HTML version deleted]]