[adegenet-forum] select loci with specific genotype in genind object

[Jombart, Thibaut]

Hello, 

yes, there are a few functions that can be helpful here. Most of them are probably documented in the 'basics' tutorial:
- 'alleles' to pull the lists of alleles for each locus
- 'locNames' to pull the locus names, with an option to get alleles too
- seploc which allows for separating loci
- []: which you can use to isolate specific loci

Example using some of these:

> data(microbov)

## list alleles per locus (just first 3)
> alleles(microbov)[1:3]
$L01
    1     2     3     4     5     6     7     8     9 
"167" "171" "173" "175" "177" "179" "181" "183" "185" 

$L02
    1     2     3     4     5     6     7 
"137" "139" "141" "143" "145" "147" "149" 

$L03
   01    02    03    04    05    06    07    08    09    10    11    12 
"137" "139" "141" "143" "145" "147" "149" "151" "153" "155" "157" "159" 


## to get loci having e.g. alleles 140:
## (TRUE = this locus has an allele "140")
> sapply(alleles(microbov), function(e) "140" %in% e)
  L01   L02   L03   L04   L05   L06   L07   L08   L09   L10   L11   L12   L13 
FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 
  L14   L15   L16   L17   L18   L19   L20   L21   L22   L23   L24   L25   L26 
FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE 
  L27   L28   L29   L30 
FALSE  TRUE FALSE FALSE 

## which loci are these?
> which(sapply(alleles(microbov), function(e) "140" %in% e))
L15 L18 L25 L28 
 15  18  25  28 

## if you want to get the position of the alleles "140" across all loci:
## this is a vector of all allele names (locus.allele)
> head(locNames(microbov, withAlleles=TRUE))
[1] "INRA63.167" "INRA63.171" "INRA63.173" "INRA63.175" "INRA63.177"
[6] "INRA63.179"

## position of those having an allele 140:
> grep("140",locNames(microbov, withAlleles=TRUE))
[1] 161 200 289 324

## there full names:
> posi <- grep("140",locNames(microbov, withAlleles=TRUE))
> locNames(microbov, withAlleles=TRUE)[posi]
[1] "BM2113.140"  "INRA37.140"  "HAUT27.140"  "TGLA122.140"


You can use this type of subsetting to isolate specific contributions.

Best
Thibaut

--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - School of Public Health
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Sara Bonanomi [bonanomi.sara85 at gmail.com]
Sent: 10 April 2014 15:26
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] select loci with specific genotype in genind object

Hi all,


In my genind object I would like to select only the loci with a certain genotype (e.g. 0102). Then I wanna check the allele contribution ($var.contr).

 If I digit: mygenindobject$all.names I get a list with xx components yielding allele names for each locus.

For instance:



$L262

   1    2

"01" "02"



Then, to get the loci only the loci with a certain genotype (e.g. 0102) , I have tried with the subset function: selectLoci<-subset(mydata$all.names, 1=="01" & 2=="02", select=c(1,2)) But then I get: named list ()

 Is there a specific function in adegenet to subset the data? Could you please help me?


Thank you very much,


Best


Jasmine