R help - Nov 2009 - Using something like the "by" command, but on rows instead of columns

Hello R Forum users,

I was hoping someone could help me with the following problem. Consider the
following "toy" dataset:

Accession    SNP_CRY2    SNP_FLC    Phenotype
1    NA    A    0.783143079
2    BQ    A    0.881714811
3    BQ    A    0.886619488
4    AQ    B    0.416893034
5    AQ    B    0.621392903
6    AS    B    0.031719125
7    AS    NA    0.652375037

"Accession" = individual plants, arbitrarily identified by unique
numbers
"SNP_" = individual genes. 
"SNP_CRY2" = the CRY2 gene. The plants either have the BQ, AQ, or AS
genotype at the CRY2 gene. "NA" = missing data.
"SNP_FLC" = the FLC gene. The plants either have the A or B genotype
at the FLC gene. "NA" = missing data.
"Phenotype" = a continuous variable of interest.

I have a much larger number of columns corresponding to genes (i.e., more
columns with the "SNP_" prefix) in my real dataset. For each gene in
turn (i.e., each "SNP_" column), I would like to find the phenotypic
variance for all of the plants with non-missing data. Note that the plants with
missing genotype data ("NA") differ for each gene (each
"SNP_" column).

Would one of you be able to offer some specific code that could do this
operation? Please rest assured that I am not a student trying to elicit help
with a homework assignment. I am a post-doc with limited R skills, working with
a large genetic dataset.

Thanks very much in advance to a wonderful online community.
Sincerely,
Josh



      
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Some variation of the following might be want you want:

df=data.frame(sex=sample(1:2,100,replace=T),snp.1=rnorm(100),snp.15=runif(100))
df$snp.1[df$snp.1>1.0]<-NA; #put some missing values into the data
x=grep('^snp',names(df)); x #which columns that begin with 'snp'
apply(df[,x],2,summary)
#or
apply(df[,x],2,FUN=function(x)mean(x,na=T))

hth,
david


Josh B-3 wrote:
> 
> Hello R Forum users,
> 
> I was hoping someone could help me with the following problem. Consider
> the following "toy" dataset:
> 
> Accession    SNP_CRY2    SNP_FLC    Phenotype
> 1    NA    A    0.783143079
> 2    BQ    A    0.881714811
> 3    BQ    A    0.886619488
> 4    AQ    B    0.416893034
> 5    AQ    B    0.621392903
> 6    AS    B    0.031719125
> 7    AS    NA    0.652375037
> 
> "Accession" = individual plants, arbitrarily identified by unique
numbers
> "SNP_" = individual genes. 
> "SNP_CRY2" = the CRY2 gene. The plants either have the BQ, AQ, or
AS
> genotype at the CRY2 gene. "NA" = missing data.
> "SNP_FLC" = the FLC gene. The plants either have the A or B
genotype at
> the FLC gene. "NA" = missing data.
> "Phenotype" = a continuous variable of interest.
> 
> I have a much larger number of columns corresponding to genes (i.e., more
> columns with the "SNP_" prefix) in my real dataset. For each gene
in turn
> (i.e., each "SNP_" column), I would like to find the phenotypic
variance
> for all of the plants with non-missing data. Note that the plants with
> missing genotype data ("NA") differ for each gene (each
"SNP_" column).
> 
> Would one of you be able to offer some specific code that could do this
> operation? Please rest assured that I am not a student trying to elicit
> help with a homework assignment. I am a post-doc with limited R skills,
> working with a large genetic dataset. 
> 
> Thanks very much in advance to a wonderful online community.
> Sincerely,
> Josh
> 
> 
> 
>       
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
> 
> 
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