R help - Nov 2010 - newbie question on importing and parsing file by row

Hi,

I'm new to R and I have a file with many rows of values. Each row contains a
title and values for a contingency table
e.g.

row 1= title	8	0	37796	47
which is a table called 'title'
with values
8     0
37796 47

I would like to know how I can import this using R and for each row calculate a
p value using the fisher test. Using each p value I will do multiple a
correction.

I am unsure how to automate this process.

Many thanks,
Emily

	[[alternative HTML version deleted]]

Hello, Emily,

take a look at read.table() for importing (with or without header 
depending on your file which holds the data). Maybe

X <- read.table( "yourfilename", header = FALSE, row.names = 1)

and then

pvalues <- apply( X, 1,
                   function( x)
                    fisher.test( matrix( x, 2, 2))$p.value
                 )

does the job (if all the data in your file are such that fisher.test() can 
cope with them ...).

Hth  --  Gerrit


On Fri, 5 Nov 2010, Emily Wong wrote:
> Hi,
>
> I'm new to R and I have a file with many rows of values. Each row 
> contains a title and values for a contingency table e.g.
>
> row 1= title	8	0	37796	47
> which is a table called 'title'
> with values
> 8     0
> 37796 47
>
> I would like to know how I can import this using R and for each row 
> calculate a p value using the fisher test. Using each p value I will do 
> multiple a correction.
>
> I am unsure how to automate this process.
>
> Many thanks,
> Emily
>
> 	[[alternative HTML version deleted]]
>
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