DDPNA (version 0.4.1)

dataStatInf: dataStatInf

Description

summrize the statistics information of data

Usage

dataStatInf(prodata, group, intensity = "intensity",
            Egrp = NULL, Cgrp = "ctl",
            meanmethod = "mean", datatype = c("none", "log2"),
            anova = TRUE, T.test = c("pairwise", "two-sample", "none"),
            Aadj = "none", Tadj = "none", cutoff = FALSE, ...)

Value

a data.frame of protein ID and Statistics information.

Arguments

prodata

proteome data. a list Vector which contain two data.frame: ID information and quantification data

intensity

the data.frame name only contain quantification data

group

sample group information

Egrp

experiment group name. It must be assigned when use Student T.test.

Cgrp

control group name. It must be assigned. The default value is "ctl".

meanmethod

Arithmetic mean of sample group or median of sample group. This must be (an abbreviation of) one of the strings "mean","median".

datatype

The quantification data is normal data or log2 data.

anova

a logical value indicating whether do anova analysis.

T.test

T.test method. "none" means not running t.test. "pairwise" means calculate pairwise comparisons between group levels with corrections for multiple testing "two-sample" means student t test. This must be (an abbreviation of) one of the strings "pairwise","two-sample and "none"".

Aadj

anova P value adjust methods. it can seen in p.adjust.methods.

Tadj

T test P value adjust methods. it can seen in p.adjust.methods.

cutoff

a logical value or a numeric value. The default value is FALSE, which means do not remove any P value. If the value is TRUE, P value > 0.05 will remove and showed as NA in result. If the value is numeric, P value > the number will remove and showed as NA in result.

...

Other arguments.

Author

Kefu Liu

Examples

data(imputedData)
group <- gsub("[0-9]+","", colnames(imputedData$intensity))
data <- imputedData
data$inf <- data$inf[1:100,]
data$intensity <- data$intensity[1:100,]
stat <- dataStatInf(data, group, meanmethod = "median",
                    T.test = "pairwise", Aadj = "fdr",
                    Tadj = "fdr", cutoff = FALSE)