Thank you so much.
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Hello to all
I have a list of invasive genes, on the other hand I have a DEG table, now I want to know if my list of genes is in the DEG table or not? How can I do this in R? With what code?
Thanks in advance
You could use intersect(). Assuming invasive is a vector of invasive genes and df is your DEG table containing a column gene, you would do :
intersect(invasive, df$gene)
Thank you so much.
You can use the %in% operator in R to ask "is this in that"? The result will be a boolean vector, which you can use to return any positions of your data frame that are TRUE. For example:
# create a data frame with 2 columns of experimental results
DEgenes <- data.frame(exp1_FC=rnorm(20), exp2_FC=rnorm(20))
# assign gene names to the rows
rownames(DEgenes) <- paste0("g", 1:nrow(DEgenes))
# make a vector of invasive genes
invasive <- c("g3", "g7", "g11", "g3145")
# Are any of the DE genes in our invasive vector?
DEgenes[rownames(DEgenes) %in% invasive,]
exp1_FC exp2_FC
g3 -0.04853683 -0.8079399
g7 -0.21303331 0.3234412
g11 0.30011850 -0.2239166
Thanks a lot.
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instead of subsetting, just do an enrichment testing.
Thank you.