protViz (version 0.7.9)

mascot: 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 mascot
is(object, class2)
  # S3 method for mascot
plot(x, ...)
  
  # S3 method for mascot
as.data.frame(x, ...)
  
  # S3 method for mascot
summary(object, ...)
  
  # S3 method for mascot_query
is(object, class2)
    
  # S3 method for mascot_query
plot(x, obj = NULL, FUN = defaultIon, ...)

Value

returns the peakplot return value.

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.

Author

Christian Panse, 2017

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.

References

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

See Also

• summary.mascot

• peakplot

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

Examples

if (FALSE) {
  # 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])
  
}