Drift time, Retention time, Intensity of GCIMSSamples — GCIMSSample-rtime-dtime-intensity • GCIMS

Functions to extract the drift time, the retention time and the intensity.

# S4 method for class 'GCIMSSample'
dtime(object)

# S4 method for class 'GCIMSSample'
rtime(object)

# S4 method for class 'GCIMSSample'
intensity(
  object,
  dt_range = NULL,
  rt_range = NULL,
  dt_idx = NULL,
  rt_idx = NULL
)

# S4 method for class 'GCIMSSample'
intensity(object) <- value

Arguments

object: A GCIMSSample object.
dt_range: The minimum and maximum drift times to extract (length 2 vector)
rt_range: The minimum and maximum retention times to extract (length 2 vector)
dt_idx: A numeric vector with the drift time indices to extract (or a logical vector of the length of drift time)
rt_idx: A numeric vector with the retention time indices to extract (or a logical vector of the length of retention time)
value: A matrix of dimensions dim(object)

Value

The drift time of the sample

The retention time of the sample

Functions

dtime(GCIMSSample): Get the drift time vector
rtime(GCIMSSample): Get the retention time vector
intensity(GCIMSSample): Get the intensity matrix
intensity(GCIMSSample) <- value: Set the intensity matrix

Examples

mea_file <- system.file("extdata",  "sample_formats", "small.mea.gz", package = "GCIMS")
gcims_sample <- read_mea(mea_file)
my_matrix <- intensity(gcims_sample, dt_range = c(7, 8), rt_range = c(1,30))
mea_file <- system.file("extdata",  "sample_formats", "small.mea.gz", package = "GCIMS")
gcims_sample <- read_mea(mea_file)
my_matrix <- intensity(gcims_sample)
intensity(gcims_sample) <- my_matrix/100