如何根据特定条件过滤行？

Question

I have an example file as follows:

GENES Samp1 Samp2 Samp3 Samp4 Samp5 Samp6 Samp7 Samp8
g1    0.000 0.000 0.000 0.000 0.010 0.000 0.022 0.344
g2    0.700 0.000 0.000 0.000 0.000 0.000 0.000 0.000
g3    0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
g4    0.322 0.782 0.000 0.023 0.000 0.000 0.000 0.345
g5    0.010 0.000 0.333 0.000 0.000 0.000 0.011 0.000
g6    0.000 0.000 0.010 0.000 0.000 0.000 0.000 0.000

I need to retrieve the list of rows (genes) if it has "2 or more samples" with the values "0.010 or more". So I should get the resulting column as follows.:

GENES
g1
g4
g5

Can anyone help me with this ?

Answer 1

Here's one possible way:

DF <- read.table(text=
"GENES Samp1 Samp2 Samp3 Samp4 Samp5 Samp6 Samp7 Samp8
g1 0.000 0.000 0.000 0.000 0.010 0.000 0.022 0.344
g2 0.700 0.000 0.000 0.000 0.000 0.000 0.000 0.000
g3 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
g4 0.322 0.782 0.000 0.023 0.000 0.000 0.000 0.345
g5 0.010 0.000 0.333 0.000 0.000 0.000 0.011 0.000
g6 0.000 0.000 0.010 0.000 0.000 0.000 0.000 0.000",header=T,sep=' ')


rows <- sapply(1:nrow(DF),FUN=function(i){sum(DF[i,2:ncol(DF)] >= 0.01) >= 2})
subSet <- DF[rows,]

> subSet
  GENES Samp1 Samp2 Samp3 Samp4 Samp5 Samp6 Samp7 Samp8
1    g1 0.000 0.000 0.000 0.000  0.01     0 0.022 0.344
4    g4 0.322 0.782 0.000 0.023  0.00     0 0.000 0.345
5    g5 0.010 0.000 0.333 0.000  0.00     0 0.011 0.000

or similarly this:

subSet <- DF[apply(DF,1,function(x){sum(tail(x,-1) >= 0.01) >= 2}),]

or this:

subSet <- DF[rowSums(DF[,2:ncol(DF)] >= 0.01) >= 2,]

as you can see there are many ways to accomplish that :)