ms_align: Align a theoretical peptide with a mass spec

In bioarch-sjh/bacollite: Analysis of MALDI and LC-MS/MS spectral data using sequence data (mainly for collagen)

Align a theoretical peptide with a mass spec

Description

Align a theoretical peptide with a mass spec

Usage

ms_align(
  ts,
  data,
  txlim,
  gauss = NA,
  normlim = NA,
  cctitle = NA,
  doplot = F,
  verbose = F,
  ccylim = c(-0.1, 0.5)
)

Arguments

ts	theoretical spectrum peaks for a particular peptide
data	the MALDI
txlim	the range of masses over which to carry out the alignment
gauss	the level of gaussian smoothing. defaults to NA (no smoothing)
normlim	the minimum upper value that the intensities should be normalised to. Defaults to NA (no minimum)
doplot	whether to generate a plot of the alignment
verbose	whether to write messages whilst processing
ccylim	range of y axis in cross-correlation plot (defaults to [-0.1,0.5])
stats	approx ccf ksmooth lm predict

Value

a dataframe holding the following fields:

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 Oct. 7, 2022, 3:34 p.m.