permute_design: Permute the design matrix so that it is approximately...

In seqgendiff: RNA-Seq Generation/Modification for Simulation

Permute the design matrix so that it is approximately correlated with the surrogate variables.

Description

Permute the design matrix so that it is approximately correlated with the surrogate variables.

Usage

permute_design(
  design_perm,
  sv,
  target_cor,
  method = c("hungarian", "marriage")
)

Arguments

design_perm	A numeric design matrix whose rows are to be permuted (thus controlling the amount by which they are correlated with the surrogate variables). The rows index the samples and the columns index the variables. The intercept should not be included (though see Section "Unestimable Components").
sv	A matrix of surrogate variables
target_cor	A numeric matrix of target correlations between the variables in design_perm and the surrogate variables. The rows index the observed covariates and the columns index the surrogate variables. That is, target_cor[i, j] specifies the target correlation between the ith column of design_perm and the jth surrogate variable. The surrogate variables are estimated either using factor analysis or surrogate variable analysis (see the parameter use_sva). The number of columns in target_cor specifies the number of surrogate variables. Set target_cor to NULL to indicate that design_perm and the surrogate variables are independent.
method	Should we use the Gale-Shapley algorithm for stable marriages ("marriage") (Gale and Shapley, 1962) as implemented in the matchingR package, or the Hungarian algorithm (Papadimitriou and Steiglitz, 1982) ("hungarian") as implemented in the clue package (Hornik, 2005)? The Hungarian method almost always works better, so is the default.

Value

A list with two elements:

design_perm

A row-permuted version of the user-provided design_perm.

latent_var

A matrix of the latent variables on which design_perm was matched.

Author(s)

David Gerard

References

• Gale, David, and Lloyd S. Shapley. "College admissions and the stability of marriage." The American Mathematical Monthly 69, no. 1 (1962): 9-15. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1080/00029890.1962.11989827")}.

• C. Papadimitriou and K. Steiglitz (1982), Combinatorial Optimization: Algorithms and Complexity. Englewood Cliffs: Prentice Hall.

• Hornik K (2005). "A CLUE for CLUster Ensembles." Journal of Statistical Software, 14(12). \Sexpr[results=rd]{tools:::Rd_expr_doi("10.18637/jss.v014.i12")}. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.18637/jss.v014.i12")}.

seqgendiff documentation built on June 22, 2024, 7 p.m.