sigrepExp {IMGTStatClonotype}R Documentation

Significance of the difference in proportions with 95% confidence interval (CI) for IMGT clonotype (AA) expression between two sets from IMGT/HighV-QUEST output

Description

This function tests the significance of the difference in proportions with 95% confidence interval (CI) for IMGT clonotype (AA) expression.

Usage

sigrepExp(Data, data1, data2)

Arguments

Data

the matrix issued from the function clonNumExp containing the number of IMGT clonotypes (AA)

data1

the first set from the IMGT/HighV-QUEST output without CDR3-IMGT outlier lengths issued from the function clonRem

data2

the second set from the IMGT/HighV-QUEST output without CDR3-IMGT outlier lengths issued from the function clonRem

Value

A matrix of 21 columns:

Gene_Name

The list of IMGT gene names found in the two compared sets from the IMGT/HighV-QUEST output

Gene_Type

The type of genes (V, D or J)

Nb_IMGT_clonotype_AA.set1

The nb of sequences assigned to IMGT clonotypes (AA) in the first IMGT/HighV-QUEST output (set) with the corresponding gene indicated in the first column "Gene_Name"

Proportion.set1

The proportion of sequences assigned to IMGT clonotypes (AA) in the first IMGT/HighV-QUEST output (set) with the corresponding gene indicated in the first column "Gene_Name"

Normalized_proportion.set1

The normalized proportion for 10000 sequences assigned to IMGT clonotypes (AA) in the first IMGT/HighV-QUEST output (set) with the corresponding gene indicated in the first column "Gene_Name"

Nb_IMGT_clonotype_AA.set2

The nb of sequences assigned to IMGT clonotypes (AA) in the second IMGT/HighV-QUEST output (set) with the corresponding gene indicated in the first column "Gene_Name"

Proportion.set2

The proportion of sequences assigned to IMGT clonotypes (AA) in the second IMGT/HighV-QUEST output (set) with the corresponding gene indicated in the first column "Gene_Name"

Normalized_proportion.set2

The normalized proportion for 10000 sequences assigned to IMGT clonotypes (AA) in the second IMGT/HighV-QUEST output (set) with the corresponding gene indicated in the first column "Gene_Name"

Difference_proportion

The difference in proportions of sequences assigned to IMGT clonotypes (AA) in the two compared sets from the IMGT/HighV-QUEST output with the corresponding gene indicated in the first column "Gene_Name"

z

The z-score values to determine the significance of the difference between two proportions

Lower_bound_IC_diff_prop

The lower bound of the 95% confidence interval (CI) for the difference in proportions of sequences assigned to IMGT clonotypes (AA) in the two compared sets from the IMGT/HighV-QUEST output

Upper_bound_IC_diff_prop

The upper bound of the 95% confidence interval (CI) for the difference in proportions of sequences assigned to IMGT clonotypes (AA) in the two compared sets from the IMGT/HighV-QUEST output

rawp

The p-values obtained from z-scores to evaluate the significance of difference in proportions of sequences assigned to IMGT clonotypes (AA) in the two compared sets from the IMGT/HighV-QUEST output

Bonferroni

The adjusted p-values issued from the Bonferroni multiple testing procedure

Holm

The adjusted p-values issued from the Holm multiple testing procedure

Hochberg

The adjusted p-values issued from the Hochberg multiple testing procedure

SidakSS

The adjusted p-values issued from the Sidak single-step (SS) multiple testing procedure

SidakSD

The adjusted p-values issued from the Sidak single-down (SD) multiple testing procedure

BH

The adjusted p-values issued from the Benjamini & Hochberg (BH) multiple testing procedure

BY

The adjusted p-values issued from the Benjamini & Yekutieli (BY) multiple testing procedure

Test_interpretation

The test interpretation: before adjustment of p-values (rawp) non-significant and after adjustment by the multiple testing procedure: significant differences in proportions validated by the seven procedures (All_p), by two or more procedures (Min_2p) and only by BH (Only_BH)

Source

Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., et al. (2004) Bioconductor: Open software development for computational biology and bioinformatics R. Genome Biology, Vol. 5, R80, https://www.bioconductor.org/

References

Pollard K.S., Dudoit S., van der Laan M.J. (2005). Multiple testing procedures: R multtest package and applications to genomics. In: Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Gentleman R., Carey V.J., Huber W., Irizarry R.A., Dudoit S. (Eds) Springer (Statistics for Biology and Health Series), pp. 251-272.

Examples


exp<-sigrepExp(Nexp,MID1,MID2)



[Package IMGTStatClonotype version 1.0.3 Index]