mascot: Generic methods for mascot results

In protViz/protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

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(object, class2)

  ## 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(object, class2)
    
  ## 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.
class2	dummy
...	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)

protViz/protViz documentation built on Jan. 19, 2024, 8:10 a.m.