multiBigwig_summary {ALPS} | R Documentation |
multiBigwig_summary
is a function to calculate
enrichments from a set of given bigwig files
and a set of genomics regions.
This function is similar to
deeptools multiBigwigSummary
python package.
multiBigwig_summary(data_table, summary_type = "mean", parallel = TRUE)
data_table |
a dataframe that contains |
summary_type |
whether to calculate mean, median, min or max
for each genomic region in within consensus peak-set
from the bigwig files. Default is |
parallel |
logical. Whether to parallelize the calculation process,
default is |
data.frame of enrichments within given genomic regions
## load example data chr21_data_table <- system.file('extdata/bw', 'ALPS_example_datatable.txt', package = 'ALPS', mustWork = TRUE) ## attach path to bw_path and bed_path d_path <- dirname(chr21_data_table) chr21_data_table <- read.delim(chr21_data_table, header = TRUE) chr21_data_table$bw_path <- paste0(d_path, '/', chr21_data_table$bw_path) chr21_data_table$bed_path <- paste0(d_path, '/', chr21_data_table$bed_path) enrichments <- multiBigwig_summary(data_table = chr21_data_table, summary_type = 'mean', parallel = FALSE)