get_variable_regions: Get variable regions

In ALPS: AnaLysis routines for ePigenomicS data

Description

given a data.frame of genomic regions enrichments, the function returns the number of variable regions across all samples. The resulting matrix can be directly used with PCAtools or ComplexHeatmap for further downstream explorative analysis e.g. unsupervised clustering

Usage

get_variable_regions(enrichments_df, log_transform = TRUE,
  scale = TRUE, num_regions = 500)

Arguments

enrichments_df	a data.frame o enrichments at genomic regions. Output of multiBigwig_summary or a similar format is compatible
log_transform	logical, whether to log2 transform the counts, default TRUE
scale	logical, whether to scale the variable regions before returning the results, default TRUE
num_regions	number of variable regions to return, default 500

Value

a data.frame of scaled variable regions

Examples

mat <- matrix(sample.int(15, 9*100, TRUE), 9, 100) %>% as.data.frame()
mat <- mat %>%
tibble::rowid_to_column(var = 'start') %>%
dplyr::mutate(end = start + 1000) %>%
dplyr::mutate(chr = 'chr1') %>%
dplyr::select(chr, start, end, dplyr::everything())

get_variable_regions(enrichments_df = mat, num_regions = 50)

ALPS documentation built on Nov. 8, 2020, 5:52 p.m.