functional-plots: hmpWindow (Currently in development and not used)

In ococrook/hdxstats: Statistical analysis of hydrogen deuterium exchange mass spectrometry

hmpWindow (Currently in development and not used)

Description

A manhatten plot for a multi-level testing prodcedure based on the haromonic mean p-value

A manhattan plot for epitope mapping

Generate an epitope map by plotting the signifcantly changed peptides with respect to a differential HDX-MS experiment

Usage

hmpWindow(params, sequences, region, interval = 20)

manhattanplot(params, sequences, difference = 0, region = NULL, nrow = 1)

plotEpitopeMap(
  AAString,
  peptideSeqs,
  numlines = 5,
  maxmismatch = 0,
  by = 5,
  scores = NULL,
  name = "-log10 p values",
  threshold = -log10(0.05)
)

plotEpitopeMapFdr(
  AAString,
  peptideSeqs,
  numlines = 5,
  maxmismatch = 0,
  by = 5,
  scores = NULL,
  name = "-log10 p values",
  threshold = -log10(0.05)
)

plotEpitopeMapResidue(
  AAString,
  peptideSeqs,
  numlines = 5,
  maxmismatch = 0,
  by = 5,
  scores = NULL,
  name = "-log10 p values",
  threshold = -log10(0.05)
)

ComputeAverageMap(
  AAString,
  peptideSeqs,
  numlines = 5,
  maxmismatch = 0,
  by = 5,
  scores = NULL,
  name = "-log10 p values",
  threshold = -log10(0.05)
)

plotAverageMaps(averageMaps, name = "-log10 p value", numlines = 2, by = 5)

forestPlot(params, condition = c(1, 2))

hdxdifference(
  object,
  AAString,
  peptideSeqs,
  numlines = 5,
  maxmismatch = 0,
  by = 5,
  cols = c(1, 4),
  scores = NULL,
  name = "-log10 p value"
)

hdxheatmap(
  averageMaps,
  diffMaps,
  name = "-log10 p value (signed)",
  numlines = 2,
  by = 5
)

Arguments

params	An object of class HdxStatRes
sequences	A character vector containing the measured peptides sequences, if there are different charge states the vector must identify the charge state.
region	The start and end of the sequences provided. Columns must be called "Start" and "End".
interval	interval size to average over.
difference	A numeric vector with deuterium differences for each peptide
nrow	The number of rows to plot the manhatten plot over. Useful for larger proteins
AAString	An object of class AAString for the protein of interest
peptideSeqs	A character vector of peptide sequences
numlines	The number of lines to plot the protein over. Useful for larger proteins. Default is 2.
maxmismatch	A numeric indicating if incorrect mapping is allowed. Number indicated the number of mismatched amino acids. Default is 0.
by	A value to indicate the legend breaks. Default is NULL.
scores	A numeric vector indicating score to be used for plotting. Most likely adjusted p-values.
name	The name of the legend for the score plotting. Default is "-log10 p values (singed)". Indicated the significance and direction
threshold	The threshold used to determine significance. Default is -log10(0.05). Note the log scale.
averageMaps	A list of average maps generated by the computeAverageMaps function
condition	If there are multiple conditions which ones to plot. Default is c(1,2)
object	An object of class QFeatures contains the hdx data.
cols	Columns for which to compute the difference. The difference is relative to the first entry.
diffMaps	A list of difference maps generated by the hdxdifference function

Value

use for side effect which returns manhattan plot

use for side effect which returns manhatten plot

Side effect produces a forest plot

ococrook/hdxstats documentation built on Sept. 15, 2022, 12:24 p.m.