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Last data update: 2014.03.03

R: Function to apply t-test separately for all peptides of each...

applyttestPep

R Documentation

Function to apply t-test separately for all peptides of each protein

Description

Generate fold changes and p-values for each protein (col 1) determined by a number of peptides (col 2).

Usage

applyttestPep(peptides, Group, doLogs = TRUE, numerator = levels(as.factor(Group))[1])

Arguments

`peptides`	Data frame with two descriptive columns: proteins, peptides, then data in the remaining ncol - 2 columns.
`Group`	Factor describing data membership. Must have two levels, and length = ncol(mat) - 2.
`doLogs`	TRUE/FALSE, log-transform data prior to analysis
`numerator`	The group level used as the numerator in the fold change.

Value

Data frame with rows Protein, fold change and p-value.

Examples


# make random matrix with first 10 proteins differentially expressed
mat = exp(6+matrix(rnorm(6000), ncol=6))
Protein = sort(paste("P", sample(1:300, 1000, replace=TRUE)))
Peptide = paste("Pep", 1:1000)
for (j in 1:10) mat[Protein == unique(Protein)[j], 4:6] = 3*mat[Protein == unique(Protein)[j], 1:3]

res = applyttestPep(data.frame(Protein, Peptide, mat), rep(c("A", "B"), each=3), numerator="B")
# first 10 proteins should have fold change 3
plot(log(res$FC), -log(res$pval), col=rainbow(2)[1+ as.numeric(1:1000 > 10)])

# add some missing values
mat[5:20,4] = NA
res = applyttestPep(data.frame(Protein, Peptide, mat), rep(c("A", "B"), each=3), numerator="B")
# first 10 proteins should have fold change 3
plot(log(res$FC), -log(res$pval), col=rainbow(2)[1+ as.numeric(1:1000 > 10)])

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(SwathXtend)
Loading required package: e1071
Loading required package: openxlsx
Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SwathXtend/applyttestPep.Rd_%03d_medium.png", width=480, height=480)
> ### Name: applyttestPep
> ### Title: Function to apply t-test separately for all peptides of each
> ###   protein
> ### Aliases: applyttestPep
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
> 
> 
> # make random matrix with first 10 proteins differentially expressed
> mat = exp(6+matrix(rnorm(6000), ncol=6))
> Protein = sort(paste("P", sample(1:300, 1000, replace=TRUE)))
> Peptide = paste("Pep", 1:1000)
> for (j in 1:10) mat[Protein == unique(Protein)[j], 4:6] = 3*mat[Protein == unique(Protein)[j], 1:3]
> 
> res = applyttestPep(data.frame(Protein, Peptide, mat), rep(c("A", "B"), each=3), numerator="B")
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
> # first 10 proteins should have fold change 3
> plot(log(res$FC), -log(res$pval), col=rainbow(2)[1+ as.numeric(1:1000 > 10)])
> 
> # add some missing values
> mat[5:20,4] = NA
> res = applyttestPep(data.frame(Protein, Peptide, mat), rep(c("A", "B"), each=3), numerator="B")
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
Error in t.test.default(log(v)) : not enough 'x' observations
> # first 10 proteins should have fold change 3
> plot(log(res$FC), -log(res$pval), col=rainbow(2)[1+ as.numeric(1:1000 > 10)])
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>