In mooredf22/spectralanalysis: compare spectral count data

knitr::opts_chunk$set(echo = TRUE)

Introduction to spectral count data

This package is designed to compare protein spectral count data derived from an experiment comparing two samples.

Installing the spectralanalysis package

This package requires the qvalue package in Bioconductor. The following commands check for the presence of the Bioconductor installation facility

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")

Now install the qvalue package from Bioconductor:

BiocManager::install("qvalue")

Since the spectralanalysis package is on github, before installing it we must install the devtools package from CRAN, by typing

install.packages("devtools")

Then install the spectralanalysis package from the github repository by typing

devtools::install_github("mooredf22/spectralanalysis")

We also will need the Hmisc package:

install.packages("Hmisc")

Now attach the spectralanalyze, qvalue, and Hmisc packages:

library(spectralanalysis)
library(qvalue)
library(Hmisc)

We may inspect the data set spectralData_ClN1_late as follows:

str(spectralData_CLN1_late)

We may examine the names as follows:

names(spectralData_CLN1_late)

Now we may extract the values for animal 1 as follows:

clnWt1 <- spectralData_CLN1_late[,c(1,2,8)]
head(clnWt1)
proteincount <- clnWt1 

Give a list of odds (and odds ratios) to test as null hypotheses:

odds.list <- c(1,2)

Now compare the cln and wt groups:

result <- proteinCountCompare(proteincount)

The function returns a list of data frames: 1. Wilson 95% confidence intervals 2. P-values for each protein based on a binomial comparison 3. Q-values for these 4. P-values for each protein based on Fisher's exact test 5. Q-values for these

names(result)
head(result$wilson.AB)
head(result$pval.AB)
head(result$qval.AB)
head(result$fisher.odds)
head(result$pval.AB.f)
head(result$qval.AB.f)

protein.mult.pval <- data.frame(proteincount," ",result$wilson.AB," ",result$pval.AB," ",
            result$qval.AB," ",result$fisher.odds," ",
            result$pval.AB.f," ",result$qval.AB.f)
head(protein.mult.pval)

We may write out the results to an external directory as follows:

setwd("c:\\temp")
write.csv(protein.mult.pval,file="Cln1Wt1.csv", row.names=F)

mooredf22/spectralanalysis documentation built on Dec. 21, 2021, 9:03 p.m.