hmpWindow  R Documentation 
A manhatten plot for a multilevel testing prodcedure based on the haromonic mean pvalue
A manhattan plot for epitope mapping
Generate an epitope map by plotting the signifcantly changed peptides with respect to a differential HDXMS experiment
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 )
params 
An object of class 
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 
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 pvalues. 
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

averageMaps 
A list of average maps generated by the 
condition 
If there are multiple conditions which ones to plot. Default
is 
object 
An object of class 
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 
use for side effect which returns manhattan plot
use for side effect which returns manhatten plot
Side effect produces a forest plot
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