init: init function of InDePTH.

In koido/InDePTH: influential gene detection in perturbed transcriptome hierarchical network

Description

init_fun is ONLY requried for the first time of InDePTH analysis in your computer. It may use large memory and a lot of time (maybe more than a day). Following files must be set in the input.dir:

zspc_n1328098x22268.gctx / level4 zspc data, provided from the lincscloud.org.

q2norm_n1328098x22268.gctx / level3 q2norm data, provided from the lincscloud.org.

inst.info / data description file, provided from the lincscloud.org.

l000-chem-pert-20413 (1).xlsx / chemical information file obtained from http://support.lincscloud.org/hc/en-us/article_attachments/200662686/l000-chem-pert-20413__1_.xlsx

HG-U133_Plus_2.na34.annot.csv / HG-U133_Plus_2 Annotations, CSV format, Release 34, obtained from Affymetrix.com support page.

Usage

init(input.dir, out.dir)

Arguments

input.dir	a character string naming a directory containing input files.
output.dir	a character string naming a directory for output files from this function.

Author(s)

Masaru Koido ([e-mail])

References

M. Koido, et al., 'Detection of hub genes for developing gene expression networks under anticancer drug treatment', *Oncotarget*, 9(49), 29097-29111, 2018.

http://www.lincsproject.org/

Examples

## Not run:
init( input.dir = "input", out.dir = "init" )
## End(Not run)

koido/InDePTH documentation built on May 28, 2019, 9:50 a.m.