Phenotype input file

[AmruthaJNC]

I am unable to create a phenotype input file. I tried creating a normal text file with two column for sample Ids and phenotype. I also tried creating a vector in R with just the phenotypes, but it is asking for sample Ids. Can i get some help in understanding how to create the phenotype file? I see that the example phen file given is a factor. This might not be a difficult problem, but I'm new to R. So any help will be appreciated.

[caitiecollins]

Hi Amrutha,

It sounds like your sample IDs may not be getting assigned as names to your phenotype.
Does names(phen) return NULL? names(phen) should contain your sample IDs.

Have you checked out the example for Loading (phenotypic) data in the Wiki?:
https://github.com/caitiecollins/treeWAS/wiki/2.-Data-&-Data-Cleaning#loading-data

If your sample IDs are a column in your text file, you probably need to do something like this to load and format your data:

## (Generating example data:)
library(treeWAS)
data(phen)
df <- data.frame("sampleID"=names(phen), "phen"=as.vector(phen))
write.table(df, file="./phen_eg.txt")

## Load, format phen:
## Read file:
df <- read.table(file="./phen_eg.txt")
## Get phen vector/factor:
phen <- df$phen
## Assign individual names to phen:
names(phen) <- df$sampleID

Please let me know if that works.
Best,
Caitlin.