How many columns can be selected in a data frame in R? - r

Question

I want to select 3117 columns out of a data frame,
I tried to select them by column names:
dataframe %>%
select(
'AAACCTGAGCACGCCT-1',
'AAACCTGAGCGCTTAT-1',
'AAACCTGAGCGTTGCC-1',
......,
'TTGGAACCACGGACAA-1'
)
or
firstpickupnames <- ('AAACCTGAGCACGCCT-1','AAACCTGAGCGCTTAT-1','AAACCTGAGCGTTGCC-1',......,'TTGGAACCACGGACAA-1')
Both ways the R console just replied
'AAACCTGAGCACGCCT-1','AAACCTGAGCGCTTAT-1','AAACCTGAGCGTTGCC-
1',......,'TTGGAACCACGGACAA-1'
+ )
+
What does this mean? Is there a limitation of columns that I can select in R?

Answer 1

Without a reproducible example, it's difficult to know what exactly you're looking for, but dplyr::select() has several options for selecting columns, and dplyr::everything() might be what you're looking for:
library(dplyr)
# this reorders the column names, but keeps everything without having to name the columns specifically:
mtcars %>%
select(carb, gear, everything())
# from a list of column names:
keep_columns <- c('cyl','disp','hp')
mtcars %>%
select(one_of(keep_columns))
# specific names, and a range of names:
mtcars %>%
select(hp, qsec:gear)
#You could also use `contains()`, `starts_with()`, `ends_with()`, or `matches()`. Note that calling all of the following at once will give you no results:
mtcars %>%
select(contains('t')) %>%
select(starts_with('a')) %>%
select(ends_with('b')) %>%
select(matches('^m.+g$'))

Answer 2

The way that the console replies (with the + indicating that it is waiting for the rest of the expression) strongly suggests that you are encountering a limitation in the capacity for the console to process long commands (which you are attempting to assemble via pasting from the clipboard) rather than an inherent limit in the number of columns which can be selected. The only place I could find in the documentation to this limitation is here where it says "Command lines entered at the console are limited to about 4095 bytes."
In the comments you said that the column names that you wanted to select were in a csv file. You didn't say much about the structure of the csv file, but say that you have a csv file that contains a single list of column names. As an example, I created a file named "colnames.csv" which has a single line:
Sepal.Width, Petal.Length
Note that there is no need to manually place quote marks around the column names in the text file. Then in the R console I typed:
iris %>% select(one_of(as.character(read.csv("colnames.csv",header = FALSE, strip.white = TRUE,stringsAsFactors = FALSE))))
which worked as expected. Even though this example only used 2 columns, there is no reason that it should fail with 3000+, since the number of columns per se wasn't the problem with what you were doing.
If the structure of the csv file is different from the example then you would need to adjust the call to read.csv and perhaps the way that you convert it to a character vector, but you should be able to tweak this approach to your situation.