sigrepDiv {IMGTStatClonotype} | R Documentation |
This function tests the significance of the difference in proportions with 95% confidence interval (CI) for IMGT clonotype (AA) diversity.
sigrepDiv(Data, data1, data2)
Data |
the matrix issued from the function |
data1 |
the first set from IMGT/HighV-QUEST output without CDR3-IMGT outlier lengths issued from the function |
data2 |
the second set from IMGT/HighV-QUEST output without CDR3-IMGT outlier lengths issued from the function |
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) |
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/
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.
div<-sigrepDiv(Ndiv,MID1,MID2)