sigrepDiv {IMGTStatClonotype} | R Documentation

## Significance of the difference in proportions with 95% confidence interval (CI) for IMGT clonotype (AA) diversity 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) diversity.

### Usage

    sigrepDiv(Data, data1, data2)

### Arguments

`Data` | the matrix issued from the function `clonNumDiv` containing the number of IMGT clonotypes (AA)
`data1` | the first set from IMGT/HighV-QUEST output without CDR3-IMGT outlier lengths issued from the function `clonRem`
`data2` | the second set from 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 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 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 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 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 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 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 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 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 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 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

     div<-sigrepDiv(Ndiv,MID1,MID2)

[Package IMGTStatClonotype version 1.0.3 Index]