ms_fit: Match a set of peptides with a Mass Spec

Description Usage Arguments Value

View source: R/ms_fit.R

Description

Match a set of peptides with a Mass Spec

Usage

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ms_fit(peptides, sample, doplot = T, force = F, vlevel = 0, corlim = 0,
  laglim = 0.6, gauss = NA, ionlim = NA, ignore_warnings = F,
  use_ms_iso = T)

Arguments

peptides

the set of peptides, in bacollite format

sample

the MS sample data, in bacollite format - three replicates required

doplot

boolean to say if the fit should be plotted

force

boolean to say if *all* fits should be calculated, instead of just the good matches

vlevel

verbose level. 0 means no comments, 3 means full comments

corlim

threshold for correlation scores

laglim

threshold for lag scores

gauss

the level of gaussian smoothing. defaults to NA (no smoothing)

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ionlim

the fraction of the highest intensity that is used to calculate the scaling limit for ms_align

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ignore_warnings

whether to ignore the check for the input and calculated mass

Value

a dataframe holding the following fields:

hit

Whether a match was found for this peptide

lag1

The lag for sample 1

lag2

The lag for sample 2

lag3

The lag for sample 3

cor1

The correlation coefficient for sample 1

cor2

The correlation coefficient for sample 2

cor3

The correlation coefficient for sample 3

ion1

The proportion of total ions for this peptide in sample 1

ion2

The proportion of total ions for this peptide in sample 2

ion3

The proportion of total ions for this peptide in sample 3


bioarch-sjh/bacollite documentation built on Dec. 13, 2018, 10:28 p.m.