targetResolve: resolving target space of drugs

In mengchen18/omic3plus: Different methods for the integrative analysis multiple omics data

Description

resolving target space and identify biomarkers by integrating drug target, cell line sensitivity and cell line molecular data

Usage

targetResolve(t, s, m, ncomp = 1, center = TRUE, scale = TRUE,
  option = "uniform", kt = "all", km = "all", wt = 1, wm = 1,
  pos = FALSE, ncores = 1, fold = 5, init = "average", nstart = 1,
  seed = NULL, loorss = FALSE, scan = FALSE, nsd = 1, verbose = TRUE)

Arguments

t	target matrix in the form target (rows) x drug (columns), values should be the higher the more potent, e.g. pKD.
s	the sensitivity matrix, in the form drug (rows) x cell line (columns), the higher the more sensitive (e.g. -log10(GI50))
m	a list of matrices, abundance of molecular features in the form of variables (rows) x cell lines (columns)
ncomp	the number of components want to retain
center	logical values, whether the variables should be centered
scale	logical values, whether the variables should be scaled
option	the option for normalizing matrix
kt	the number (if it is an integer >= 1) or the proportion (if 0 < kt < 1) of kept variables in t. It should be a numeric value.
km	the number (if it is an integer >= 1) or the proportion (if 0 < km < 1) of kept variables in m. It should be a numeric value.
wt	weight for the rows of t
wm	weight for the rows of m
pos	logical value, whether only non-negative loadings retained
ncores	number of cores to be used, passed to mclapply
fold	the number of fold to be used in cross-validation, only used if kx or ky is a vector
init	how to initialize the algorithm. if no sparsity, svd is fast.
nstart	how many time the k-fold cross validation should be done
seed	set seed for random number generation
loorss	if the Leave-one-out procedure should be used in matrix reconstruction
scan	If the PRESS plot should be shown and used to determine the optimal k in CV
nsd	the the n*sd for selecting k automatically
verbose	if the process of calculation should be printed

Author(s)

Chen Meng

mengchen18/omic3plus documentation built on May 6, 2019, 4:59 p.m.