Inconsistencies in "Importing custom data formats" vignette

[forsterepi]

Dear GCIMS team,
we tried to use your package with csv files and followed your instructions in the "Importing custom data formats" vignette. We ran into some inconsistencies, however, and are not entirely sure, where the error is.
In the vignette, the intensity() function, which extracts the intensity from the GCIMSSample object, puts the drift times in the first column, i.e., the "rownames". This seems to be in accordance with your description of the intensity matrix as a matrix with length(drift_time) rows. However, in the code you select the top row from the input data, i.e., the "colnames" as the drift times. There is no error in the example, because the input data is symmetrical, but as you can see in the reprex below, when I add another column, there is an error related to the indexes (It wants to select 6 rows, but there are only 5). Where exactly is the error here? Are the definition of retention_time and drift_time the wrong way round?

Reprex:

library(GCIMS)
library(withr)

# Original input
your_csv_file <- (
  ",0.0,0.1,0.2,0.3,0.4
0.0,  0, 20, 80, 84, 23
0.8,123,200,190,295, 17
1.6,230,300,200, 92, 15
2.4,120,150,120, 33, 22
3.2, 70,121, 74, 31, 34
")

csv_data <- withr::with_tempfile("path", fileext = ".csv", {
  write(your_csv_file, path)
  read.csv(path, check.names = FALSE)
})

retention_time <- csv_data[[1]]
drift_time <- as.numeric(colnames(csv_data)[-1])
intensity <- as.matrix(csv_data[,-1])
rownames(intensity) <- retention_time

s1 <- GCIMSSample(
  drift_time = drift_time, 
  retention_time = retention_time,
  data = intensity
)

intensity(s1)
#>      rt_s
#> dt_ms   0 0.8 1.6 2.4 3.2
#>   0     0  20  80  84  23
#>   0.1 123 200 190 295  17
#>   0.2 230 300 200  92  15
#>   0.3 120 150 120  33  22
#>   0.4  70 121  74  31  34
intensity
#>     0.0 0.1 0.2 0.3 0.4
#> 0     0  20  80  84  23
#> 0.8 123 200 190 295  17
#> 1.6 230 300 200  92  15
#> 2.4 120 150 120  33  22
#> 3.2  70 121  74  31  34

# Add column
your_csv_file <- (
  ",0.0,0.1,0.2,0.3,0.4, 0.5
0.0,  0, 20, 80, 84, 23, 1
0.8,123,200,190,295, 17, 2
1.6,230,300,200, 92, 15, 3
2.4,120,150,120, 33, 22, 4
3.2, 70,121, 74, 31, 34, 5
")

csv_data <- withr::with_tempfile("path", fileext = ".csv", {
  write(your_csv_file, path)
  read.csv(path, check.names = FALSE)
})

retention_time <- csv_data[[1]]
drift_time <- as.numeric(colnames(csv_data)[-1])
intensity <- as.matrix(csv_data[,-1])
rownames(intensity) <- retention_time

s1 <- GCIMSSample(
  drift_time = drift_time, 
  retention_time = retention_time,
  data = intensity
)

intensity(s1)
#> Error in `object@data[dt_idx, rt_idx, drop = FALSE]`:
#> ! (subscript) logical subscript too long

^{Created on 2026-01-29 with reprex v2.1.1}

[zeehio]

I believe you are correct. I'm on a phone and I don't have access to a computer right now but I believe the vignette is inconsistent.

According to the image above, the intensity matrix has as many rows as drift time points.

According to the image above, the first column contains the retention time.

This contradicts the first sentence.

I need to fix the vignette. Making the table with a different number of rows than columns and using really different numbers for drift and retention time, so it is clear what's the expected behaviour.

The corrected version should state:

• The first row contains the drift time vector.
• The column names contain the retention times

And the code should follow that convention.