R: Generic methods for mascot results

mascot {protViz} | R Documentation

## Generic methods for mascot results

### Description

does something with a `mascot` object using the package's functions, e.g., `peakplot` or `lcmsmap`.

### Usage

      ## S3 method for class 'mascot'
    is(obj)

      ## S3 method for class 'mascot'
    plot(x, ...)

      ## S3 method for class 'mascot'
    as.data.frame(x, ...)

      ## S3 method for class 'mascot'
    summary(object, ...)

      ## S3 method for class 'mascot_query'
    is(obj)

      ## S3 method for class 'mascot_query'
    plot(x, obj = NULL, FUN = defaultIon, ...)

### Arguments

`x` | a `mascot_query` or `mascot` S3 class object.
`object` | a `mascot` S3 class object.
`obj` | a `mascot` S3 class object.
`...` | arguments will be passwed through.
`FUN` | ion series.

### Details

the object has been generated by using the mascot server command `./export_dat_2.pl $EXPORTOPTIONS file=$DAT`.

`$EXPORTOPTIONS` is defined as `"_minpeplen=5 _server_mudpit_switch=0.000000001 _showsubsets=1 _sigthreshold=0.05 do_export=1 export_format=XML group_family=1 pep_calc_mr=1 pep_delta=1 pep_end=1 pep_exp_mr=1 pep_exp_mz=1 pep_exp_z=1 pep_expect=1 pep_isbold=1 pep_isunique=1 pep_miss=1 pep_query=1 pep_rank=1 pep_scan_title=1 pep_score=1 pep_seq=1 pep_start=1 pep_var_mod=1 peptide_master=1 prot_acc=1 prot_cover=1 prot_desc=1 prot_empai=1 prot_hit_num=1 prot_len=1 prot_mass=1 prot_matches=1 prot_pi=1 prot_score=1 prot_seq=1 protein_master=1 query_master=1 query_params=1 query_peaks=1 query_qualifiers=1 query_raw=1 query_title=1 search_master=1 show_format=1 show_header=1 show_masses=1 show_mods=1 show_params=1 show_pep_dupes=1 use_homology=1 user=command line"`.

`$DAT` defines the mascot result file.

The output is written as XML file the following command is applied: `XML::xmlToList(XML::xmlParse(xml_file_name))`.

xmlParse and xmlToList are function of the XML package.

### Value

returns the peakplot return value.

### Author(s)

Christian Panse, 2017

### References

http://www.matrixscience.com/mascot_support_v2_6.html

### See Also

- `summary.mascot`

- `peakplot`

- https://CRAN.R-project.org/package=XML

### Examples

    ## Not run:
      # plot the top ten highes scored PSMs
      par(ask = TRUE)
      idx <- order(protViz:::.mascot.get.pep_score(S), decreasing = TRUE)[1:10]
      rv.peakplot <- lapply(S$queries[idx], plot)

      myAA <- do.call('rbind', lapply(F225712$masses,
        function(x){
          data.frame(letter1=as.character(x$.attrs), mass=as.numeric(x$text))
          }))

      aa2mass("ELVISR", mass=myAA$mass[1:25], letter1 = myAA$letter1[1:25])

    ## End(Not run)

[Package protViz version 0.2.45 Index]