Compute distance between a protein group of
interest and assess its significance by comparing it to the distances
of randomly selected groups of proteins.
Numeric matrix containing the protein data to analyze.
index
Protein identifiers for the protein group
of interest in the data set ‘values’, as returned from
‘grepAnnotation’ or an equivalent function.
nSample
Integer specifying the number of randomly selected
groups of proteins with the same number of elements as specified by
‘index’, serving as a reference for the significance
assessment (default: 1000).
seed
Random seed, relevant for the permutation step. For
details, see the ‘seed’ function.
z
Return object from ‘profileDistance.’
...
Optional arguments passed to the ‘plot’ function.
Value
List with elements:
d0
Numeric with mean distance d_0 of profiles for the proteins of interest.
d1
Vector of numerics with mean distances d_1 of randomly selected groups of proteins.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(proteinProfiles)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/proteinProfiles/profileDistance.Rd_%03d_medium.png", width=480, height=480)
> ### Name: profileDistance
> ### Title: profileDistance
> ### Aliases: profileDistance plotProfileDistance
>
> ### ** Examples
>
>
> data(ips_sample)
>
> index_28S <- grepAnnotation(annotation, pattern="^28S",
+ column="Protein.Name")
>
> z <- profileDistance(ratios, index_28S)
>
> z$p.value
[1] 0.584
>
> plotProfileDistance(z)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.