#1

I'm trying to declare the following variable as a list of patient ID's to use for further analysis:

id = c("patientID1", "patientID2", ...)

I have a list of about 5000 patient ID's I need to do this for, so I used a comma separated list generator. The minimal working example given in this Stack post works, but when I try it for all of my patient ID's it doesn't seem to work. Importantly, when I tried the minimal working example in the Stack post (it worked), I did type it out manually rather than using the column to list converter.

Any ideas here? Is there another way that I should be making the comma separated list in R from an excel column to make sure that it works? Why is R giving me the + sign anyways? The brackets are closed.

#2

The console has a character limit.
Put your excel column into CSV format and read the CSV file into R

#3

Thank you very much! Can I declare the variable "id" as the column in Excel? Are there any guides to this? Apologies, I'm new to R.

#4

Typically the first row of a CSV is a header and users to name the column that will be made from the following rows beneath it. any read CSV function would support that. Also you can rename columns later.

#5

When I use id <- read.csv(file.choose(), header=T) I get an error in the next thing that I want to do:

> filtered <- data_rs146217251[id,]
Error in data_rs146217251[id, ] : invalid subscript type 'list'

I want to import the .csv column exactly as this:

> id <- c("4428814_4428814", "3490518_3490518", "3094358_3094358")
> id
[1] "4428814_4428814" "3490518_3490518"
[3] "3094358_3094358"

So that I can run this:

> filtered <- data_rs146217251[id,]
> filtered
                g=0 g=1 g=2
4428814_4428814   0   0   1
3490518_3490518   0   0   1
3094358_3094358   0   0   1

How do I import the .csv column in a format that would be precisely in the same form as the c() function, as in id <- c("4428814_4428814", "3490518_3490518", "3094358_3094358"), rather than the list that read.csv() gives?

#6

Where does your data_rs146217251 come from ?
The first thing you do is read the CSV into an object called id.

Secondly I don't understand where the g= information is supposed to have come from if you are loading only a list of ids?

#7

The data_rs146217251 comes from a main dataset called data which has a bunch of different genetic data. The g= information comes from a different file that I loaded from a .bgen file using the rbgen package (it's allele dosage data), but that's unrelated.

Here's a post which explains exactly what I'm trying to do, and for which there is a solution which I'm trying to use: https://stackoverflow.com/questions/61965995/extracting-rows-in-r-based-on-an-id-number

I tried id <- read.csv(file.choose(), header=T) using the .csv file with the list of patient ID's, but then as soon as I ran > filtered <- data_rs146217251[id,] it gave me the error Error in data_rs146217251[id, ] : invalid subscript type 'list'.

So that's why I'd prefer a way that I could just load the column from the .csv in a way that replicates the same vectorized form that's given by

> id <- c("4428814_4428814", "3490518_3490518", "3094358_3094358")
> id
[1] "4428814_4428814" "3490518_3490518"
[3] "3094358_3094358"

Does that help clarify what I'm trying to do?

#8

Apologies, I was able to figure out my problem. What I did was:

df <- read.csv('C:\\Path\\To\\DataFile.csv')
id <- df[[1]]

to import the column as a vector and that worked!

Thank you for your help again.

1 Like
#9

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.