HBP (version 0.1.2)

calculate_omiccircos_data: output the interaction that our bed interact with ourbed.

Description

output the interaction that our bed interact with ourbed.

Arguments

cmap

bed_matrix

bed_bin

bedfile

chr

st_cmap

m_threshold

Examples

# NOT RUN {
##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (cmap, bed_matrix, bed_bin, bedfile, chr = "chr4", st_cmap,
    m_threshold = 0)
{
    n = dim(cmap)[1]
    bed_count = 0
    nm_count = 0
    all_count = 0
    cccc = 0
    ooo <- data.frame(chr_nm1 = character(0), n_start1 = numeric(0),
        bed_seq1 = character(0), chr_nm2 = character(0), n_start2 = numeric(0),
        bed_seq2 = character(0), read_count = numeric(0), stringsAsFactors = FALSE)
    ooo = lapply(rbind(1:(dim(bed_matrix)[1] - 1)), calculate_omiccircos_data_solo,
        cmap = cmap, bed_matrix = bed_matrix, bed_bin = bed_bin,
        bedfile = bedfile, chr = chr, st_cmap = st_cmap, m_threshold = m_threshold)
    final_ooo <- data.frame(chr_nm1 = character(0), n_start1 = numeric(0),
        bed_seq1 = character(0), chr_nm2 = character(0), n_start2 = numeric(0),
        bed_seq2 = character(0), read_count = numeric(0), stringsAsFactors = FALSE)
    for (tt in 1:(dim(bed_matrix)[1] - 1)) {
        if (!is.null(ooo[tt][[1]])) {
            final_ooo = rbind(final_ooo, as.data.frame(ooo[tt][[1]]))
        }
    }
    colnames(final_ooo) = c("chr_nm1", "n_start1", "bed_seq1",
        "chr_nm2", "n_start2", "bed_seq2", "read_count")
    return(final_ooo)
  }
# }