Get identification table from a metIdentifyClass object

Source: R/deprecated_functions.R

Get identification table from a metIdentifyClass object. [Deprecated]

getIdentificationTable(..., candidate.num = 3, type = c("old", "new"))

Arguments

...

One or multiple metIdentifyClass objects.

candidate.num

The number of candidates.

type

The type of identification table.

Value

A identification table (data.frame).

See also

The example and demo data of this function can be found https://jaspershen.github.io/metID/articles/metID.html

Author

Xiaotao Shen shenxt1990@163.com

Examples

data("annotate_result", package = "metID")
annotation_table <- 
getIdentificationTable(annotate_result, candidate.num = 3, type = "old")
#> `getIdentificationTable()` is deprecated, use `get_identification_table()`.
annotation_table
#> # A tibble: 100 × 6
#>    name          mz    rt MS2.spectra.name       Candidate.number Identification
#>    <chr>      <dbl> <dbl> <chr>                             <dbl> <chr>         
#>  1 pRPLC_376   472. 773.  NA                                    0 NA            
#>  2 pRPLC_391   466. 747.  NA                                    0 NA            
#>  3 pRPLC_603   162.  33.7 mz162.112442157672rt3…                1 Compound.name…
#>  4 pRPLC_629   181.  36.4 NA                                    0 NA            
#>  5 pRPLC_685   230. 158.  NA                                    0 NA            
#>  6 pRPLC_722   181. 228.  mz181.072050304971rt2…                1 Compound.name…
#>  7 pRPLC_778   289. 286.  mz289.227264404297rt2…                0 NA            
#>  8 pRPLC_1046  181. 201.  mz181.072050673093rt1…                3 Compound.name…
#>  9 pRPLC_1112  209.  57.4 mz209.092155077047rt5…                1 Compound.name…
#> 10 pRPLC_1148  283.  40.9 NA                                    0 NA            
#> # … with 90 more rows
annotation_table <- 
getIdentificationTable(annotate_result, candidate.num = 3, type = "new")
#> `getIdentificationTable()` is deprecated, use `get_identification_table()`.
annotation_table
#> # A tibble: 115 × 17
#>    name  mz    rt    Compound.name CAS.ID HMDB.ID KEGG.ID Lab.ID Adduct mz.error
#>    <chr> <chr> <chr> <chr>         <chr>  <chr>   <chr>   <chr>  <chr>  <chr>   
#>  1 pRPL… "472… "772… NA            NA     NA      NA      NA     NA     NA      
#>  2 pRPL… "466… "746… NA            NA     NA      NA      NA     NA     NA      
#>  3 pRPL… "162… " 33… L-Carnitine   541-1… HMDB00… C00318  RPLC_… (M+H)+ 1.66789…
#>  4 pRPL… "181… " 36… NA            NA     NA      NA      NA     NA     NA      
#>  5 pRPL… "230… "158… NA            NA     NA      NA      NA     NA     NA      
#>  6 pRPL… "181… "228… Theophylline  NA     HMDB00… NA      RPLC_… (M+H)+ 1.68826…
#>  7 pRPL… "289… "286… NA            NA     NA      NA      NA     NA     NA      
#>  8 pRPL… "181… "201… Theophylline  611-5… HMDB01… C07130  RPLC_… (M+H)+ 2.43918…
#>  9 pRPL… ""    ""    Paraxanthine  611-5… HMDB01… C13747  RPLC_… (M+H)+ 1.93918…
#> 10 pRPL… ""    ""    Theophylline  NA     HMDB00… NA      RPLC_… (M+H)+ 1.68918…
#> # … with 105 more rows, and 7 more variables: mz.match.score <chr>,
#> #   RT.error <chr>, RT.match.score <chr>, CE <chr>, SS <chr>,
#> #   Total.score <chr>, Database <chr>