[R] how to calculate multiple meta p values

[Michael Dewey]

Dear Ana

Yes, when apply coerces q to a matrix it does so as a character matrix 
because of the values in the first column. So you need to wrap the 
references to x in helper in as.numeric() tat is to day like 
as.numeric(x[2:4]) and similarly for the other one. Sorry about that, I 
should have thought of it before.

When I next update metap I will try to get it to degrade more gracefully 
when it finds an error.

Michael

On 28/10/2019 19:06, Ana Marija wrote:
> Hi Michael,
> 
> I tried what you proposed with my data frame q:
> 
>> head(q)
>             ID                P             G              E
>   wb          wg           we
> 1:  rs1029830 0.0979931 0.0054060 0.39160 580.6436 40.6325 35.39774
> 2:  rs1029832 0.1501820 0.0028140 0.39320 580.6436 40.6325 35.39774
> 3: rs11078374 0.1701250 0.0009805 0.49730 580.6436 40.6325 35.39774
> 4:  rs1124961 0.1710150 0.7252000 0.05737 580.6436 40.6325 35.39774
> 5:  rs1135237 0.1493650 0.6851000 0.06354 580.6436 40.6325 35.39774
> 6: rs11867934 0.0757972 0.0006140 0.00327 580.6436 40.6325 35.39774
> 
> so the solution of the first row would be this:
>> sumz(c(0.0979931,0.0054060,0.39160), weights = c(580.6436,40.6325,35.39774), na.action = na.fail)
> sumz =  1.481833 p =  0.06919239
> 
> I tried applying the function you wrote:
> helper <- function(x) {
>    p <- sumz(x[2:4], weights = x[5:7])$p
>    p
> }
> 
> With:
> 
> q$META <- apply(q, MARGIN = 1, helper)
> 
> # I want to make a new column in q named META with results
> but I got this error:
>   Error in sumz(x[2:4], weights = x[5:7]) :
>    Must have at least two valid p values
> 
> Please advise,
> Ana
> 
> On Sun, Oct 27, 2019 at 9:49 AM Michael Dewey <lists using dewey.myzen.co.uk> wrote:
>>
>> Dear Ana
>>
>> There must be several ways of doing this but see below for an idea with
>> comments in-line.
>>
>> On 26/10/2019 00:31, Ana Marija wrote:
>>> Hello,
>>>
>>> I would like to use this package metap
>>> to calculate multiple o values
>>>
>>> I have my data frame with 3 p values
>>>> head(tt)
>>>             RS            G           E          B
>>> 1: rs2089177   0.9986   0.7153   0.604716
>>> 2: rs4360974   0.9738   0.7838   0.430228
>>> 3: rs6502526   0.9744   0.7839   0.429160
>>> 4: rs8069906   0.7184   0.4918   0.521452
>>> 5: rs9905280   0.7205   0.4861   0.465758
>>> 6: rs4313843   0.9804   0.8522   0.474313
>>>
>>> and data frame with corresponding weights for each of the p values
>>> from the tt data frame
>>>
>>>> head(df)
>>>          wg       we             wb                RS
>>> 1 40.6325 35.39774 580.6436 rs2089177
>>> 2 40.6325 35.39774 580.6436 rs4360974
>>> 3 40.6325 35.39774 580.6436 rs6502526
>>> 4 40.6325 35.39774 580.6436 rs8069906
>>> 5 40.6325 35.39774 580.6436 rs9905280
>>> 6 40.6325 35.39774 580.6436 rs4313843
>>>
>>> RS column is the same in df and tt
>>>
>>
>> So you can create a new data-frame with merge()
>>
>> newdata <- merge(tt, df)
>>
>> which will use RS as the key to merge them on.
>>
>> The write a function of one argument, a seven element vector, which
>> picks out the p-values and the weights and feeds them to sumz().
>> Something like
>>
>> helper <- function(x) {
>>    p <- sumz(x[2:4], weights = x[5:7])$p
>>    p
>> }
>> Note you need to check that 2:4 and 5:7 are actually where they are in
>> the row of newdat.
>>
>> Then use apply() to apply that to the rows of newdat.
>>
>> I have not tested any of this but the general idea should be OK even if
>> the details are wrong.
>>
>> Michael
>>
>>
>>> How to use this sunz() function to create a new data frame which would
>>> look the same as tt only it would have additional column, say named
>>> "META" which has calculated meta p values for each row
>>>
>>> This i s example of how much would be p value in the first row:
>>>
>>>> sumz(c(0.9986,0.7153,0.604716), weights = c(40.6325,35.39774,580.6436), na.action = na.fail)
>>> p =  0.6940048
>>>
>>> Thanks
>>> Ana
>>>
>>> ______________________________________________
>>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>> --
>> Michael
>> http://www.dewey.myzen.co.uk/home.html
> 

-- 
Michael
http://www.dewey.myzen.co.uk/home.html