CODEWITHSUNDEEP
rstatistics
TriRook
TriRook

Reputation: 167

unused arguments and invalid subscript type list error in R

i am struggling with an assignment and i would like your input. note: this is a homework but when i tried to add the tag it said not to add it.. i don't want the resulting code, just suggestions on how to get this working :)

so, i have a t.test function as such:

    my.t.test <- function(x,s1,s2){
        x1 <- x[s1]
        x2 <- x[s2]
        x1 <- as.numeric(x1)
        x2 <- as.numeric(x2)
        t.out <- t.test(x1,x2,alternative="two.sided",var.equal=T)
out <- as.numeric(t.out$p.value)
        return(out)
    }

a matrix 30cols x 12k rows called data and an annotation file containing col names and data on the colums named dataAnn

dataAnn first column contains a list of M (male) or F (female) corresponding to the samples (or cols) in data (that follow the same order as in dataAnn), i have to run a t.test comparing the two samples and get the p values out

when i call 

raw.pValue <- apply(data,1,my.t.test,s1=dataAnn[,1]=="M",s2=dataAnn[,1]=="F")

i get the error 

Error in t.test(x1, x2, alternative = "two.sided", var.equal = T) : 
  unused argument(s) (alternative = "two.sided", var.equal = T)

i even tried to use 

raw.pValue <- apply(data,1,my.t.test,s1=unlist(data[,1:18]),s2=unlist(data[,19:30]))

to divide the cols i want to compare but in this case i get the error

Error in x[s1] : invalid subscript type 'list'

i have been looking online, i understand that the second error is caused by an indices being a list...but this didn't really clarify it for me... any input would be appreciated!!

Upvotes: 1

Views: 3513

Answers (1)

James
James

Reputation: 66834

You have overwritten the t.test function. Try calling it something like my.t.test, or when you want to call the original one use stats::t.test (this calls the one from the stats namespace). Remember that when you have overwritten a function you need to rm it from your workspace before you can use the original one without specifying the namespace.

Upvotes: 1

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