Ranking genes based on other features

Question

[sadaf]

I have a list of genes that I want to rank them based on two other features(P&Z column) using robust rank aggregation, see below:

my_dataTable:

gene_name   P   Z
x                  6.3   0.08
y                  5.6  0.009
z                  3.4  0.04
w                   2.6 0.0085

In aggregate() method we can assign other columns to the genes, e.g. aggregate(gene_name~P+Z, my_dataTable , median), but how can I do the same in robust rank aggregation method?

could anyone help me with this?

Answer 1

[ATpoint]

How about:

my_dataTable <-
  data.frame(gene_name=c("x", "y", "z", "w"),
             P=c(6.3, 5.6, 3.4, 2.6),
             Z=c(0.08, 0.009, 0.04, 0.0085))

library(RobustRankAggreg)

#/ make the glist with the ordered gene names:
glist <- list(P=my_dataTable[order(my_dataTable$P),"gene_name"],
              Z=my_dataTable[order(my_dataTable$Z),"gene_name"])

#/ aggregate by ranks:
aR <- aggregateRanks(glist=glist)

#/ match order in aR with my_dataTable:
matched <- match(aR$Name, my_dataTable$gene_name)

#/ order my_dataTable accordingly:
my_dataTable[matched,]

[sadaf]

Thanks. I'm gonna give it a try