Hi All,
Say I have a data set with the following structure:
Lines <- "ID ref_rank R1 R2 R3 R4 R5 R6
A 6 3 NA NA 7 8 2
B 7 4 NA NA 9 5 10
C 3 7 NA NA 8 10 8
D 4 2 NA NA 4 8 1
E 2 5 NA NA 4 7 7
F 8 5 NA NA 7 10 9
G 5 9 NA NA 8 10 2
H 1 6 NA NA 7 10 10"
my.data <- read.table(con<-textConnection(Lines), header = TRUE)
close(con)
I create a function to compute Spearman's rank correlation between a
reference column named "ref_rank" and columns R1--R6, as shown below:
my.func <- function(x)
{
rc <- rcorr(my.data[,c("ref_rank")], x)
data.frame(Spearman = rc$r[2],Pval=rc$P[2])
}
I then apply the function on the desired columns as shown below:
a<-data.frame(t(sapply(my.data[, 3:8], my.func)))
I almost get what I intended to do, but I'm unable to export the data frame
"a" to CSV format. For that matter, I'm not able to remove
NA's using
na.omit(a). Here's the log:
> class(a)
[1] "data.frame"> write.csv(a,file="aranks.csv",na="")
Error in write.table(x, file, nrow(x), p, rnames, sep, eol, na, dec,
as.integer(quote), :
unimplemented type 'list' in 'EncodeElement'
I'm not sure, but I'm suspecting the problem might be in the output
structure of the my.func. Any helpful hints in resolving this is highly
appreciated.
cheers,
-Girish
> sessionInfo()
R version 2.10.1 (2009-12-14)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] splines grid stats graphics grDevices utils datasets
methods
[9] base
other attached packages:
[1] polycor_0.7-7 sfsmisc_1.0-10 mvtnorm_0.9-9 Hmisc_3.7-0
survival_2.35-7
[6] RWinEdt_1.8-2 ggplot2_0.8.5 digest_0.4.2 reshape_0.8.3
plyr_0.1.9
[11] proto_0.3-8
loaded via a namespace (and not attached):
[1] cluster_1.12.1 Formula_0.2-0 kinship_1.1.0-23 lattice_0.17-26
MASS_7.3-4
[6] nlme_3.1-96 plm_1.2-1 sandwich_2.2-5 tools_2.10.1
--
View this message in context:
http://n4.nabble.com/Help-needed-in-fine-tuning-the-sapply-output-tp1475639p1475639.html
Sent from the R help mailing list archive at Nabble.com.
