Hi there,
I would like to calculate ratio of NN (total markers/ total NN) from different groups (here 6 sample A and B-groups) in R. It must be easy but I couldn't any example online.
I have found some similar answer but as a newbie to R, I couldn't annotate the code. https://stackoverflow.com/questions/48555851/adding-a-row-for-the-ratio-of-two-variables
A1 A2 A3 A4 A5 A6 B1 B2 B3 B4 B5 B6
M1 CC CC AC AA CC CC CC AA AC CC CC CC
M2 NN AA AA AC AA AA AA AA AA AA AA AA
M3 AA AA NN NN AA AA GG NN GG GG NN NN
M4 NN NN NN AA AA NN AA AA AA AA NN NN
expected output
A1 A2 A3 A4 A5 A6 B1 B2 B3 B4 B5 B6 A-ratio B-ratio A+B-ratio
M1 CC CC AC AA CC CC CC AA AC CC CC CC - - -
M2 NN AA AA AC AA AA AA AA AA AA AA AA 0 - 11
M3 AA AA NN NN AA AA GG NN GG GG NN NN 1.5 0.7 1.4
M4 NN NN NN AA AA NN AA AA AA AA NN NN 0 4 1.0
Thanks for your help.
I am guessing we are trying to get missingness per sample and overall, try this example:
# example data
df1 <- read.table(text = " A1 A2 A3 A4 A5 A6 B1 B2 B3 B4 B5 B6
M1 CC CC AC AA CC CC CC AA AC CC CC CC
M2 NN AA AA AC AA AA AA AA AA AA AA AA
M3 AA AA NN NN AA AA GG NN GG GG NN NN
M4 NN NN NN AA AA NN AA AA AA AA NN NN", header = TRUE, stringsAsFactors = FALSE)
x <- colnames(df1)
cbind(df1,
sapply(c("A", "B"), function(i){
d <- df1[ grepl(paste0("^", i), x) ]
rowSums(d == "NN")/ncol(d)
}),
AB = rowSums(df1 == "NN")/ncol(df1)
)
# A1 A2 A3 A4 A5 A6 B1 B2 B3 B4 B5 B6 A B AB
# M1 CC CC AC AA CC CC CC AA AC CC CC CC 0.0000000 0.0000000 0.00000000
# M2 NN AA AA AC AA AA AA AA AA AA AA AA 0.1666667 0.0000000 0.08333333
# M3 AA AA NN NN AA AA GG NN GG GG NN NN 0.3333333 0.5000000 0.41666667
# M4 NN NN NN AA AA NN AA AA AA AA NN NN 0.6666667 0.3333333 0.50000000
That's what I was thinking also but the output of this doesn't match the presented expected output. Waiting for OP to clarify.
Awesome...thanks a lot @zx8754, it worked well. I will make to use dput format for future requests.
Friederike and Jean-Karim Heriche - sorry that the ratios were wrong (for missingness) in my expected output because it was from my entire data set (180x35000) as I subsampled but forgot to calculate the ratio for this subsample.
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I don't understand what A-ratio, B-ratio, A+B-ratio are supposed to represent. Can you spell out how you arrived at the values in the last three columns of the second row?