[adegenet-forum] extracting genefreq $tab from an indexed list

[Jombart, Thibaut]

Hi there,

the operator [[]] returns a slot of a list, not a list, which is an issue here. To subset a list you should use [].

Otherwise, to do what you want, you need something like:
lapply(mygenfreq, function(e) t(e$tab))

Note that as of adegnet_2.0-0, there will be a simpler interface to get frequencies (tab(x, freq=TRUE)).

Cheers
Thibaut


________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Vikram Chhatre [crypticlineage at gmail.com]
Sent: 30 March 2015 03:25
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] extracting genefreq $tab from an indexed list

I am working with hundreds of genpop objects indexed in a list.  Using lapply and makefreq functions, population gene frequencies were stored in individual objects (1 per data set).

Here is an example with just three objects:

>summary(mygenpop)
                  Length Class  Mode
data1.str 1      genpop S4
data2.str 1      genpop S4
data3.str 1      genpop S4

>mygenfreq <- lapply(mygenpop, function(x) makefreq(x, truenames=TRUE))

>summary(mygenfreq)
                  Length Class  Mode
data1.str 3      -none- list
data2.str 3      -none- list
data3.str 3      -none- list

>summary(mygenfreq[[1]]$tab)
> str(mygenfreq[[1]])
 $ tab : num [1:30, 1:1974] 0.6 0.5 0.325 0.675 0.6 0.5 0.5 0.375 0.55 0.475 ...
 $ nobs: num [1:30, 1:1000] 40 40 40 40 40 40 40 40 40 40 ...

Next job is to work with the $tab matrix, but I am not sure how to access it from all objects in one command.

>mygenfreqT <- lapply(mygenfreq[[1:3]]$tab, function(x) t(x))

This throws an error.   The syntax seems to be wrong, but I am not sure how to fix this.  Thanks for any help.

Vikram


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