R factors in a loop to build full data frame - r

Question

I'm trying to write a loop that performs anova and TukeyHSD on my data across 3 samples for each "Label". Label in this case is a metabolic pathway. Data that goes into it are the genes expressed in said metabolic pathway.
For the test data, I created a small df that reproduces my error. In my actual data, I'm hoping to do perform this across 2 factors (not just one) and I have thousands of more rows.
library(reshape2)
df<-melt(data.frame(sample1 = c(0,0,3,4,5,1),sample2 = c(1,0,0,4,5,0),sample3 = c(0,0,0,8,0,0),Label = c("TCA cycle", "TCA cycle","TCA cycle", "Glycolysis","Glycolysis","Glycolysis"),Gene = c("k1","k2","k3","k4","k5","k6")))
My approach (annotated the best way I can!):
fxn<-unique(df$Label) #create list
for (i in 1:length(fxn)){
if (!exists("data")){ #if the "data" dataframe does not exist, start here!
depth<-aov(df$value[df$Label==fxn[i]]~df$variable[df$Label==fxn[i]]) #perform anova on my "df", gene values as a factor of samples (for each "fxn")
hsd<-TukeyHSD(depth) #calculate tukeyHSD
data<-as.data.frame(hsd$`df$variable[df$Label == fxn[i]]`) #grab dataframe of tukey HSD output
data$Label<-fxn[i] #add in the Label name as a column (so it looks like my original df, but with TukeyHSD output for each pairwise comparison
data<-as.data.frame(data)
}
if (exists("data")){ #if "data" exists, do this:
tmpdepth<-aov(df$value[df$Label==fxn[i]]~df$variable[df$Label==fxn[i]])
tmphsd<-TukeyHSD(tmpdepth)
tmpdata<-as.data.frame(tmphsd$`df$variable[df$Label == fxn[i]]`)
tmpdata$Label<-fxn[i]
tmpdata<-as.data.frame(tmpdata)
data<-rbind(data,tmpdata) #combine with original data
data<-as.data.frame
rm(tmpdata)
}
}
I'd like my output to look like this:
diff lwr upr p adj Label
sample2-sample1 -0.3333333 -8.600189 7.933522 0.9916089 Glycolysis
sample3-sample1 -0.6666667 -8.933522 7.600189 0.9669963 Glycolysis
sample3-sample2 -0.3333333 -8.600189 7.933522 0.9916089 Glycolysis
but the Label column has all the factors that went into "fxn".
Errors:
Error in rep(xi, length.out = nvar) :
attempt to replicate an object of type 'closure'

Answer 1

You forgot the second data in the last line before rm(tmpdata). It should be:
data<-as.data.frame(data)
I my implementation I changed your code as follows:
datav <- data.frame(diff = double(),
lwr = double(),
upr = double(),
'p adj' = double(),
'Label' = character())
for (fxn in unique(df$Label)){
depth <- aov(df$value[df$Label==fxn] ~ df$variable[df$Label==fxn])
hsd <- TukeyHSD(depth)
tmp <- as.data.frame(hsd$`df$variable[df$Label == fxn]`)
tmp$Label <- fxn
datav <- rbind(datav, tmp)
}
Initializing the data.frame before hand you do not need the if statement. Also data is a function in R, so I rename the variable data to datav.