array2: Data 2 for CCP+RF+ vs Control peptide array.

In ZihaoZheng-Stat/MixTwice_Package: A package for large-scale hypothesis testing utilizing high density peptide array

Usage

data("array2")

Format

A data frame with 152603 observations on the following 16 variables.

First 12 columns are CCP+RF+ RA patients and the last columns are healthy controls

Details

The peptides in this data set is same as that in array1. However, the signals are evaluated independently are from different subjects.

Source

Zheng, Zihao, et al. Disordered Antigens and Epitope Overlap Between Anti Citrullinated Protein Antibodies and Rheumatoid Factor in Rheumatoid Arthritis. Arthritis & Rheumatology 72.2 (2020): 262-272.

References

https://onlinelibrary.wiley.com/doi/abs/10.1002/art.41074

See Also

See Also as help(array1), help(mixtwice)

Examples

## load the RA data

data(array2)

## z-score

get_zscore = function(x){
  
  x1 = x[1:length(x)/2]
  x2 = x[(length(x)/2+1):length(x)]
  
  t = t.test(x1, x2, var.equal = T)$statistic
  
  z = qnorm(pt(t, df = length(x)-2))
  
  return(z)
}

z2 = apply(array2, 1, get_zscore)

## visualize z-score

hist(z2, probability = T, col = "blue", 100)
lines(density(rnorm(10^5)), lty = 2, lwd = 2)

ZihaoZheng-Stat/MixTwice_Package documentation built on Oct. 13, 2020, 1:23 a.m.