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Extract EEM samples

Source: R/eem_utils.R
eem_extract.Rd

Extract EEM samples

Usage

eem_extract(eem, sample, keep = FALSE, ignore_case = FALSE, verbose = TRUE)

Arguments

eem

An object of class eemlist.

sample

Either numeric of character vector. See details for more information.

keep

logical. If TRUE, the specified sample will be returned. If FALSE, they will be removed.

ignore_case

Logical, should sample name case should be ignored (TRUE) or not (FALSE). Default is FALSE.

verbose

Logical determining if removed/extracted eems should be printed on screen.

Value

An object of class eemlist.

Details

sample argument can be either numeric or character vector. If it is numeric, samples at specified index will be removed.

If sample is character, regular expression will be used and all sample names that have a partial or complete match with the expression will be removed. See examples for more details.

Examples

folder <- system.file("extdata/cary/scans_day_1", package = "eemR")
eems <- eem_read(folder, import_function = "cary")

eems
#>    sample ex_min ex_max em_min em_max is_blank_corrected is_scatter_corrected
#> 1    nano    220    450    230    600              FALSE                FALSE
#> 2 sample1    220    450    230    600              FALSE                FALSE
#> 3 sample2    220    450    230    600              FALSE                FALSE
#> 4 sample3    220    450    230    600              FALSE                FALSE
#>   is_ife_corrected is_raman_normalized
#> 1            FALSE               FALSE
#> 2            FALSE               FALSE
#> 3            FALSE               FALSE
#> 4            FALSE               FALSE

# Remove first and third samples
eem_extract(eems, c(1, 3))
#> Removed sample(s): nano sample2 
#>    sample ex_min ex_max em_min em_max is_blank_corrected is_scatter_corrected
#> 1 sample1    220    450    230    600              FALSE                FALSE
#> 2 sample3    220    450    230    600              FALSE                FALSE
#>   is_ife_corrected is_raman_normalized
#> 1            FALSE               FALSE
#> 2            FALSE               FALSE

# Remove everything except first and third samples
eem_extract(eems, c(1, 3), keep = TRUE)
#> Extracted sample(s): nano sample2 
#>    sample ex_min ex_max em_min em_max is_blank_corrected is_scatter_corrected
#> 1    nano    220    450    230    600              FALSE                FALSE
#> 2 sample2    220    450    230    600              FALSE                FALSE
#>   is_ife_corrected is_raman_normalized
#> 1            FALSE               FALSE
#> 2            FALSE               FALSE

# Remove all samples containing "3" in their names.
eem_extract(eems, "3")
#> Removed sample(s): sample3 
#>    sample ex_min ex_max em_min em_max is_blank_corrected is_scatter_corrected
#> 1    nano    220    450    230    600              FALSE                FALSE
#> 2 sample1    220    450    230    600              FALSE                FALSE
#> 3 sample2    220    450    230    600              FALSE                FALSE
#>   is_ife_corrected is_raman_normalized
#> 1            FALSE               FALSE
#> 2            FALSE               FALSE
#> 3            FALSE               FALSE

# Remove all samples containing either character "s" or character "2" in their names.
eem_extract(eems, c("s", "2"))
#> Removed sample(s): sample1 sample2 sample3 
#>   sample ex_min ex_max em_min em_max is_blank_corrected is_scatter_corrected
#> 1   nano    220    450    230    600              FALSE                FALSE
#>   is_ife_corrected is_raman_normalized
#> 1            FALSE               FALSE

# Remove all samples containing "blank" or "nano"
eem_extract(eems, c("blank", "nano"))
#> Removed sample(s): nano 
#>    sample ex_min ex_max em_min em_max is_blank_corrected is_scatter_corrected
#> 1 sample1    220    450    230    600              FALSE                FALSE
#> 2 sample2    220    450    230    600              FALSE                FALSE
#> 3 sample3    220    450    230    600              FALSE                FALSE
#>   is_ife_corrected is_raman_normalized
#> 1            FALSE               FALSE
#> 2            FALSE               FALSE
#> 3            FALSE               FALSE