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Read one or more spectra from Disk

Source: R/10_spec.R
read_spectrum.Rd

read_spectrum() reads a single spectrum from disk and returns it as spectrum object. read_spectra() can be used to read multiple spectra at once and returns a spectra object.

Usage

read_spectrum(
  data_path = metabodecon_file("bruker/sim/sim_01"),
  file_format = "bruker",
  expno = 10,
  procno = 10,
  raw = FALSE,
  silent = TRUE,
  force = FALSE
)

Arguments

data_path

The path of the file/folder containing the spectrum data. E.g. "example_datasets/jcampdx/urine/urine_1.dx" or "example_datasets/bruker/urine/urine".

file_format

The file_format of the spectrum file. E.g. "bruker" or "jcampdx".

expno, procno

The experiment/processing number for the file. E.g. "10". Only relevant if file_format equals "bruker". For details see section File Structure in the metabodecon FAQ.

raw

If FALSE, scales the returned signal intensities based on information available in the spectrum metadata, in particular NC_proc. For details see processing-reference.pdf, available at https://www.bruker.com/en.html at section 'Services & Support > Documentation & Manuals > Magnetic Resonance > Acquisition & Processing > TopSpin Processing Commands and Parameters' (requires login).

silent

If TRUE, no output will be printed to the console.

force

If TRUE, try to continue when encountering errors and print info messages instead. To hide these messages as well, set silent = TRUE.

Value

A spectrum object as described in metabodecon_classes.

Examples

relpath <- "example_datasets/bruker/urine"
urine <- system.file(relpath, package = "metabodecon")
urine_1 <- file.path(urine, "urine_1")
urine_2 <- file.path(urine, "urine_2")
x1 <- read_spectrum(urine_1)
x2 <- read_spectrum(urine_2)
xx <- read_spectra(urine)
str(xx)
#> List of 2
#>  $ urine_1:List of 3
#>   ..$ si  : num [1:131072] 316.2 250.8 26.2 -234.2 -265.5 ...
#>   ..$ cs  : num [1:131072] 14.8 14.8 14.8 14.8 14.8 ...
#>   ..$ meta:List of 6
#>   .. ..$ fq    : num [1:131072] 6e+08 6e+08 6e+08 6e+08 6e+08 ...
#>   .. ..$ name  : chr "urine_1"
#>   .. ..$ path  : chr "/home/runner/work/_temp/Library/metabodecon/example_datasets/bruker/urine/urine_1"
#>   .. ..$ type  : NULL
#>   .. ..$ simpar: NULL
#>   .. ..$ mfs   : NULL
#>   ..- attr(*, "class")= chr "spectrum"
#>  $ urine_2:List of 3
#>   ..$ si  : num [1:131072] -1544 -1464 -1416 -1436 -1398 ...
#>   ..$ cs  : num [1:131072] 14.8 14.8 14.8 14.8 14.8 ...
#>   ..$ meta:List of 6
#>   .. ..$ fq    : num [1:131072] 6e+08 6e+08 6e+08 6e+08 6e+08 ...
#>   .. ..$ name  : chr "urine_2"
#>   .. ..$ path  : chr "/home/runner/work/_temp/Library/metabodecon/example_datasets/bruker/urine/urine_2"
#>   .. ..$ type  : NULL
#>   .. ..$ simpar: NULL
#>   .. ..$ mfs   : NULL
#>   ..- attr(*, "class")= chr "spectrum"
#>  - attr(*, "class")= chr "spectra"
str(x1)
#> List of 3
#>  $ si  : num [1:131072] 316.2 250.8 26.2 -234.2 -265.5 ...
#>  $ cs  : num [1:131072] 14.8 14.8 14.8 14.8 14.8 ...
#>  $ meta:List of 6
#>   ..$ fq    : num [1:131072] 6e+08 6e+08 6e+08 6e+08 6e+08 ...
#>   ..$ name  : chr "urine_1"
#>   ..$ path  : chr "/home/runner/work/_temp/Library/metabodecon/example_datasets/bruker/urine/urine_1"
#>   ..$ type  : NULL
#>   ..$ simpar: NULL
#>   ..$ mfs   : NULL
#>  - attr(*, "class")= chr "spectrum"
stopifnot(all.equal(x1, xx$urine_1))