Calculate the difference betwen pairs of consecutive rows in a data frame - R

Question

I have a data.frame in which each gene name is repeated and contains values for 2 conditions:

df <- data.frame(gene=c(\"A\",\"A\",\"B\",\"B\",\"C\",\"C\"),
c         


        

Answer 1

The plyr solution would look something like:

library(plyr)
reg.fun <- function(x) {
  reg.diff <- x$count[x$condition=='control'] - x$count[x$condition=='treatment']
  x$regulation <- ifelse(reg.diff > 0, 'up', 'down')

  x
}

ddply(df, .(gene), reg.fun)


  gene condition count  sd regulation
1    A   control    10 1.0         up
2    A treatment     2 0.2         up
3    B   control     5 0.1       down
4    B treatment     8 2.0       down
5    C   control     5 0.8         up
6    C treatment     1 0.1         up
> 

You could also think about doing this with a different package and/or with data in a different shape:

df.w <- reshape(df, direction='wide', idvar='gene', timevar='condition')

library(data.table)
DT <- data.table(df.w, key='gene')

DT[, regulation:=ifelse(count.control-count.treatment > 0, 'up', 'down'), by=gene]

   gene count.control sd.control count.treatment sd.treatment regulation
1:    A            10        1.0               2          0.2         up
2:    B             5        0.1               8          2.0       down
3:    C             5        0.8               1          0.1         up
>     

Answer 2

Something like this:

df$up.down <- with( df, ave(count, gene,
                FUN=function(diffs) c("up", "down")[1+(diff(diffs) < 0) ]) )
spltdf <- split(df, df$up.down)

> df
  gene condition count  sd up.down
1    A   control    10 1.0    down
2    A treatment     2 0.2    down
3    B   control     5 0.1      up
4    B treatment     8 2.0      up
5    C   control     5 0.8    down
6    C treatment     1 0.1    down
> spltdf
$down
  gene condition count  sd up.down
1    A   control    10 1.0    down
2    A treatment     2 0.2    down
5    C   control     5 0.8    down
6    C treatment     1 0.1    down

$up
  gene condition count  sd up.down
3    B   control     5 0.1      up
4    B treatment     8 2.0      up