diffHet: Calculate Differential Heterogeneity

In TheJacksonLaboratory/epihet: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Description

From a user-inputted value and two subtype groups, calculates the mean values for both subtypes at each loci. The heterogeneity difference is calculated and the p-values and adjusted p-values are calculated if the heterogeneity difference is greater than a given cutoff

Usage

diffHet(compare.matrix, value, group1, group2, subtype,
  het.dif.cutoff = 0.2, permutations = 1000, permutationtest = FALSE,
  p.adjust.method = "fdr", cores = 5)

Arguments

compare.matrix	The comparison matrix generated from the compMatrix() function
value	The value to be used in calculations. Possible values are 'read', 'pdr', 'meth', 'epipoly', and 'shannon'
group1	The first subtype group to be compared
group2	The second subtype group to be compared
subtype	A dataframe containing the subtype information for the samples in the comparison matrix. The row names should be the names of the samples and there should be one column containing the subtype information for each sample.
het.dif.cutoff	A number representing the cutoff for the heterogeneity difference. If the heterogeneity difference is greater than the cutoff value, than the p-value and adjusted p-value are calculated for the loci. If the heterogeneity difference is less than the cutoff value, than the p-value and adjusted p-value are set to NA. (default: 0.20)
permutations	The number of permutations for the EntropyExplorer function. Value must be set to 'shannon'. (default: 1000)
permutationtest	boolean values determining if the permutation test is applied for DEH loci identification based on customized heterogeneity metrics (default: FALSE)
p.adjust.method	The method to be used as a parameter in p.adjust() function. Possible methods are 'holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', and 'none'.(default: 'fdr')
cores	The number of cores to be used for parallel execution. Not available for 'shannon' values. (default: 5)

Value

A dataframe containing chromosome number, loci, mean of group1, mean of group2, heterogeneity difference, and the p-value and adjusted p-value for the loci with a heterogeneity difference greater than the cutoff

TheJacksonLaboratory/epihet documentation built on Dec. 22, 2020, 1:10 p.m.