[R] Pairwise comparison between columns, logic

arun smartpink111 at yahoo.com
Fri Jul 26 17:18:48 CEST 2013

Hi Manisha,
I didn't run your dataset as I am on the way to college.  But, from the error reported, I think it will be due to some missing combinations in one of the dataset.  For ex. if you run my previous code without removing CEBPA:
mat1<- combn(gset[,1],2)

lst2<-lapply(split(mat1,col(mat1)),function(x) {x1<-join_all(lst1[x],by="patient_id",type="inner");x1["patient_id"] } )
#Error: All inputs to rbind.fill must be data.frames

So, check whether all the combinations are available in the `lst1`.

2. I will get back to you once I run it.

From: Manisha <manishabh77 at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Friday, July 26, 2013 11:09 AM
Subject: Re: Pairwise comparison between columns, logic

Hi Arun,
I ran the script on a larger dataset and I seem to be running into this following error:
Error: All inputs to rbind.fill must be data.frames
after the step;
lst2<-lapply(split(mat1,col(mat1)),function(x) {x1<-join_all(lst1[x],by="firehose_patient_id",type="inner");x1["firehose_patient_id"]}) 
I tried a few things to solve the issue but I am not able to. The format of input files and data are same as in the code you posted.
Could you suggest me something?
I have attached my input files on which I am trying to run the code. See attached code as well. Minor changes have been made by me.

2. I have another question. From your code how do also capture those pairs of names that donot have any common patient id?

Thanks again,

On Fri, Jul 26, 2013 at 9:29 AM, arun <smartpink111 at yahoo.com> wrote:

Hi M,
>No problem.
>----- Original Message -----
>From: "manishabh77 at gmail.com" <manishabh77 at gmail.com>
>To: smartpink111 at yahoo.com
>Sent: Friday, July 26, 2013 9:27 AM
>Subject: Re: Pairwise comparison between columns, logic
>Thanks for the code. It is elegant and does what I need. Learnt some new things.
>Sent from http://r.789695.n4.nabble.com

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