targetResolve2: resolving target space of drugs

Description Usage Arguments Author(s)

Description

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

Usage

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targetResolve2(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.