eqtm: eqtm

In ND91/eqtm:

Usage

eqtm(dmrs_gr, gene_col, meth_data, expr_data, meth_anno_gr,
  cor_method = c("pearson", "kendall", "spearman"),
  alternative = c("two.sided", "greater", "less"), N = 1000, ncores = 1,
  iseed = NULL, verbose = T)

Arguments

dmrs_gr	A GenomicRanges-derived object where the ranges represent the coordinates of the DMR and whose metadata contains an associated gene identifier.
gene_col	A column index containing of the dmrs_gr object containing the gene identifiers.
meth_data	A matrix whose row names contain CpG identifiers and whose values represent the methylation signal. The column names must contain the columns names of the gene expression data.
expr_data	A matrix whose row names contain gene identifiers and whose values represent the expression signal. The column names must contain the columns names of the methylation data.
meth_anno_gr	A GenomicRanges-derived object where the ranges represent the coordinates of the assayed CpGs and whose rownames contain an identifier.
alternative	Alternative hypothesis to be used for calculating the p-values ("two.sided", "greater", "less").
N	The number of bootstraps and permutations for calculating the 95 \item ncoresThe number of cores to use for bootstrapping and permutations (default: 1) \item iseedA seed for the bootstrapping and permutations for reproducibility \item verboseA boolean whether the printed output should be verbose (default: T) \item cor_typeType of correlation ("pearson", "kendall", "spearman").

A SummarizedExperiment object containing the location of the summarized methylation and gene expression data for the overlapping samples. This function was setup to perform an expression quantitative trait methylation analysis for methylation and gene expression data obtained from the same samples. Andrew Y.F. Li Yim eqtm, expression methylation,

ND91/eqtm documentation built on May 17, 2019, 6:22 p.m.