I have a data object signal in R with 40,000+ rows (named variables) of numeric values and 200+ columns (samples). For every row of each column, I want to subtract the value for the row named background for that column.
The code below can be used to create an example signal object in R. With the example, for column A, the background value of 4 is to be subtracted from the values of channelNo1 to 3. Similarly, for column B, the value of 6 is to be subtracted. And so on. What is the simplest way to achieve this in R?
text <- textConnection('
A B C
channelNo1 12 22 32
channelNo2 13 21 33
channelNo3 12 21 30
background 4 6 8
')
signal <- read.table(text, header = TRUE)
close(text)
typeof(signal)
# returns 'list'
class(signal)
# returns 'data.frame'
Elements in an R matrix are oriented by column (check out matrix(1:12, nrow=3) and signal - signal[4,] is not doing what you think -- check out column B, where the second and third values should be the same (and equal to 15). You could write
as.data.frame(Map("-", signal, as.vector(signal[4,])))
(I think this would be relatively efficient) but since the data really seem to be a matrix (i.e., a rectangle of homogeneous type) it makes a lot more sense to manipulate it as a matrix
m = as.matrix(signal)
sweep(m, 2, m[4,], "-")