jackstraw (version 1.3.1)

jackstraw_lfa: Non-Parametric Jackstraw for Logistic Factor Analysis

Description

Test association between the observed variables and their latent variables captured by logistic factors (LFs).

Usage

jackstraw_lfa(
  dat,
  FUN = function(x) lfa(x, r)[, , drop = FALSE],
  devR = FALSE,
  r = NULL,
  r1 = NULL,
  s = NULL,
  B = NULL,
  covariate = NULL,
  verbose = TRUE,
  seed = NULL
)

Arguments

dat

a genotype matrix with m rows as variables and n columns as observations.

FUN

a function to use for LFA (by default, it uses the lfagen package)

devR

use a R function to compute deviance. By default, FALSE (uses C++).

r

a number of significant LFs.

r1

a numeric vector of LFs of interest (implying you are not interested in all r LFs).

s

a number of ``synthetic'' null variables. Out of m variables, s variables are independently permuted.

B

a number of resampling iterations. There will be a total of s*B null statistics.

covariate

a data matrix of covariates with corresponding n observations (do not include an intercept term).

verbose

a logical specifying to print the computational progress.

seed

a seed for the random number generator.

Value

jackstraw_lfa returns a list consisting of

p.value

m p-values of association tests between variables and their LFs

obs.stat

m observed devs

null.stat

s*B null devs

Details

This function uses logistic factor analysis (LFA) from Wei et al. (2014). Particularly, a deviation dev in logistic regression (the full model with r LFs vs. the intercept-only model) is used to assess association.

References

Chung and Storey (2015) Statistical significance of variables driving systematic variation in high-dimensional data. Bioinformatics, 31(4): 545-554 https://academic.oup.com/bioinformatics/article/31/4/545/2748186

Chung (2020) Statistical significance of cluster membership for unsupervised evaluation of cell identities https://academic.oup.com/bioinformatics/article/36/10/3107/5788523

See Also

jackstraw_pca jackstraw jackstraw_subspace

Examples

# NOT RUN {
set.seed(1234)
# }
# NOT RUN {
## simulate genotype data from a logistic factor model: drawing rbinom from logit(BL)
m=5000; n=100; pi0=.9
m0 = round(m*pi0)
m1 = m-round(m*pi0)
B = matrix(0, nrow=m, ncol=1)
B[1:m1,] = matrix(runif(m1*n, min=-.5, max=.5), nrow=m1, ncol=1)
L = matrix(rnorm(n), nrow=1, ncol=n)
BL = B %*% L
prob = exp(BL)/(1+exp(BL))

dat = matrix(rbinom(m*n, 2, as.numeric(prob)), m, n)

## apply the jackstraw_lfa
out = jackstraw_lfa(dat, 2)

## apply the jackstraw_lfa using self-contained R functions
out = jackstraw_lfa(dat, FUN = function(x) lfa.corpcor(x, 2)[, , drop = FALSE], r = 2, devR = TRUE)
# }