Amova output in csv format / accesible to R

Feature requests
1

Hi,

I am currently developping a Sweave automatic report procedure for analysis of mothur output.
I would very much like to include the amova output into my R code and pass it on to LaTeX with xtable but it is impossible to read in the *.amova files into R.
However, because of the format of the output this is not possible at the moment.
I would propose a csv/tsv like output with the following format:

Group       Calculator    Among     Within   Total
g1-g2-gn   SS                 n            n          n
g1-g2-gn   df                 n           n           n
g1-g2-gn   MS                n           n           n
g1-g2-gn   Fs                                          n
g1-g2-gn   pvalue                                   n
g1-g2-gn   EER                                       n
g1-g2-gn   PwER                                    n

Here g1-g2-gn are the pairwise or experiment wise groups that are included in the design. EER and PwER concern the experiment wise error rate and the pairwise error rate. n refers to the number calculated.

Kind regards,

Frederiek - Maarten Kerckhof

2

Hi!

It’s actually rather simple to read amova tables created by mothur to R. I created a small example function that reads just one table, and converts it to a more traditional ANOVA table. Note however that this reads just one table, e.g., the following one I took from mothur manual.

F-M Among Within Total
SS 2.10271 5.51471 7.61742
df 1 22 23
MS 2.10271 0.250669

Fs: 8.3884
p-value: <0.001*

The function is readAmova() (copy and paste the code below to your R console):

readAmova<-function(x) {
   d<-strsplit(readLines(x), "\t")
   m<-matrix(ncol=5, nrow=2, data=NA)
   rownames(m)<-c(gsub(" ", "", d[[1]][1]), "Residuals")
   colnames(m)<-c("Df", "Sum Sq", "Mean Sq", "F Value", "P Value")
   m<-data.frame(m)
   m[,1]<-as.numeric(d[[3]][2:3])
   m[,2]<-as.numeric(d[[2]][2:3])
   m[,3]<-as.numeric(d[[4]][2:3])
   m[,4]<-as.numeric(c(d[[6]][2], " "))
   m[,5]<-as.numeric(c(substr(d[[7]], 11, 15), " "))
   m
}

The usage is simple. Assuming the aforementioned table is in the file amova.txt, type in R:

readAmova("amova.txt")

The output then looks like this:

Df Sum.Sq Mean.Sq F.Value P.Value
F-M 1 2.10271 2.102710 8.3884 0.001
Residuals 22 5.51471 0.250669 NA NA

Or, if you want to output a Latex code for a similar table, use:

library(xtable)
xtable(readAmova("amova.txt"))

If you know R, you can probably modify the function to cope with several tables in the same file, also.

Best Regards,
Jarno

3

Thank you so much for helping me with this.

Kind regards,

FM