Write output of a loop

Question

I am running a loop across thousands of file to conduct a Pagel Lambda

files <- list.files(pattern=".txt")
column_names <- data.frame(files = "files", V1 = "V1", Lambda = "lamda", LogL = "logL", LogL10 = "logL10", pvalue = "P")
write.table(column_names, file = "output.csv", row.names = FALSE, 
            append = FALSE, col.names = FALSE, sep = ", ", quote = TRUE)

for(i in files){
  graph <- read.table(i,header=F)
  row.names(graph)<-graph[,1]
  trait<-graph[,-1]
  names(trait)<-row.names(graph)
  result <- data.frame(t(c(files[i], phylosig(mytree, trait, method="lambda", test=TRUE, nsim=999))))
  write.table(result, file = "output.csv", row.names = FALSE, 
              append = TRUE, col.names = FALSE, sep = ", ")
}

My goal is to get one output file with 1 line for each input file's result. My variable result looks like this:

[1] "some data in x given as 'NA', dropping corresponding species from tree"
             V1       lambda      logL     logL0 P
1 EOG7B0F7J.txt 6.610696e-05 -59.62533 -59.62509 1

I need these values to be in the output file AND the name of the input file (I did not set that yet in my loop, I have no idea how to do it)

So I would like the output to look like this:

FileA  V1       lambda      logL     logL0 P
FileB V1       lambda      logL     logL0 P
FileC V1       lambda      logL     logL0 P

Or something similar - I would be super happy if somebody could help me out with this

Thanks a lot

There is a typo in your data.frame line.

user3710546
– user3710546

2015-11-17 01:09:14 +00:00
Commented Nov 17, 2015 at 1:09 — user3710546
– user3710546, Commented Nov 17, 2015 at 1:09
True I fixed it! Thanks

user3188922
– user3188922

2015-11-17 01:12:26 +00:00
Commented Nov 17, 2015 at 1:12 — user3188922
– user3188922, Commented Nov 17, 2015 at 1:12

user3188922 · Accepted Answer · 2015-11-17 02:03:23Z

1

I figured it out, here is the answer if somebody is interested:

column_names <- data.frame(i = "files", Lambda = "lamda", LogL = "logL", LogL10 = "logL10", pvalue = "P")
                           write.table(column_names, file = "output.csv", row.names = FALSE, 
                           append = FALSE, col.names = FALSE, sep = ", ", quote = TRUE)

for(i in files){
  graph <- read.table(i,header=F)
  row.names(graph)<-graph[,1]
  trait<-graph[,-1]
  names(trait)<-row.names(graph)
  result <- data.frame(t(c(i, phylosig(mytree, trait, method="lambda", test=TRUE, nsim=999))))
  my.df <- data.frame(lapply(result, as.character), stringsAsFactors=FALSE)
  write.table(my.df, file = "output.csv", row.names = FALSE, append = TRUE, col.names = FALSE, sep = ", ")
}

answered Nov 17, 2015 at 2:03

user3188922

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