Dear all: I want to obtain chi-square statistics for following data by element wise. My apology to ask this statistical question from this community. However, my data contains list of overlap's significance score of 3 GRanges objects, I want to get its global score by element-wise. How can I get this in R?
This is the data that I want to get its global score by element wise:
[[1]]
NumericList of length 7
[[1]] 1e-22
[[2]] 1e-19
[[3]] 1e-18
[[4]] 1e-16
[[5]] 1e-24
[[6]] 1e-20
[[7]] 1e-15
[[2]]
NumericList of length 7
[[1]] 1e-24
[[2]] 1e-24
[[3]] 1e-20
[[4]] 1e-25
[[5]] 0.1
[[6]] 1e-19
[[7]] 1e-18
[[3]]
NumericList of length 7
[[1]] 1e-11
[[2]] 1e-11
[[3]] 1e-10
[[4]] numeric(0)
[[5]] numeric(0)
[[6]] 1e-15
[[7]] numeric(0)
if you wonder third list element contains numeric(0), which refers to non-overlapped regions, so I can replace it with zero:
li.3 <- <- lapply(li.3, function(x) {
res <- ifelse(length(x)>0, x, 0)
})
this is reproducible example :
data <- DataFrame(
v1=c(1e-22,1e-19,1e-18,1e-16,1e-24,1e-20, 1e-15),
v2=c(1e-24,1e-24,1e-20,1e-25,0.1,1e-19,1e-18),
v3=c(1e-11,1e-11,1e-10,numeric(0),numeric(0),1e-15,numeric(0)))
my desired output something like (just example by element wise) :
global fisher score of `(1e-22, 1e-24, 1e-11)` = ?
global fisher score of `(1e-19, 1e-24, 1e-11)` = ?
...
global fisher score of `(1e-24, 1e-01, numeric(0))` = ?
I want to get global score by element wise. How can I get this in R? Alternatively, I also prefer to see fisher exact test result for above data. I will be grateful if anyone can give me any idea for doing this. Thanks a lot
Where are the GRanges objects?
Dear Giovanni M Dall'Olio:
I afraid it would be bit of long thread if I listed all step here (from finding overlap, conditionally filtering,expand them as GRanges), so I did not show reproducible step here. However, the data that I want to get global score is from the result of some sort of filtering by element-wise. so I have to make sure its geometric property of vector. To be specific, All I want to do is to get its global Fisher scores by element wise. To be clarify,
v1
refers to significant score of query, whilev2, v3
are significance score (a.k.a, pvalueLog )of subjects (a.k.a, overlapped GRanges objects). I need to do element-wise operation to getting global score. I hope I would have some idea from this community.