modpar.new: Settings for multiSOMe analysis

In lydiahopp/multiSOMe: Integration of multiple OME data sets using SOMs

Description

Settings for multiSOMe analysis

Usage

modpar.new(modpar = NULL)

Arguments

dataset.name	all output will be stored in a folder with the name given
meth.type	type of Methylation Assay used. Either '27K' for Infinium HumanMethylation27K or 'K450' for Infinium HumanMethylation450K. If methylation data is already preprocessed and the data matrix contains methylation values per gene per sample set meth.type=""
w	weight used to either focus on gene expression (w=0), DNA methylation (w=1) or on both (w=0.5)
mean.norm.exp	enables centralization of the expression features (boolean)
mean.norm.meth	enables centralization of the methylation features (boolean)
quant.exp	enables quantile normalization of the expression samples (boolean)
quant.meth	enables quantile normalization of the expression samples (boolean)
M	enables calculation of M values out of methylation beta values (boolean)
row.ids.exp	type of rowname identifier in biomaRt database of gene expression matrix, for example 'ensembl_gene_id', "refseq_mrna" or 'external_gene_name'. For details see https://www.bioconductor.org/packages//2.7/bioc/vignettes/biomaRt/inst/doc/biomaRt.pdf
row.ids.meth	type of rowname identifier in biomaRt database of DNA methylation matrix, for example 'ensembl_gene_id', "refseq_mrna" or 'external_gene_name'. For details see https://www.bioconductor.org/packages//2.7/bioc/vignettes/biomaRt/inst/doc/biomaRt.pdf
return.ids	type of rowname identifier in biomaRt database to return, for example 'ensembl_gene_id' or 'external_gene_name'. For details see https://www.bioconductor.org/packages//2.7/bioc/vignettes/biomaRt/inst/doc/biomaRt.pdf

Value

modpar

lydiahopp/multiSOMe documentation built on Oct. 13, 2019, 2:06 p.m.