Convert an interval-indexed matrix back to an intervals + values data.frame

Source: R/intervals-to-mat.R

Inverse of gintervals.to_mat. Recovers intervals from attr(mat, "intervals") if mat is an intervs_mat, or from the explicit intervals argument if mat is a plain matrix. Never parses rownames.

gintervals.from_mat(mat, intervals = NULL)

Arguments

mat

an intervs_mat (produced by gintervals.to_mat) or a plain matrix (then intervals must be supplied).

intervals

data.frame with chrom, start, end columns, required when mat is a plain matrix. Must satisfy nrow(intervals) == nrow(mat); alignment is strictly positional. Must NOT be supplied when mat is already an intervs_mat.

Value

A data.frame with chrom, start, end (plus intervalID if it was present in the original input), followed by the value columns.

Examples

df <- data.frame(
    chrom = c("chr1", "chr2"),
    start = c(100L, 200L),
    end   = c(200L, 400L),
    t1    = c(1.0, 2.0)
)
mat <- gintervals.to_mat(df)
identical(gintervals.from_mat(mat)$t1, df$t1)
#> [1] TRUE

# plain matrix path:
plain <- unclass(mat)
attr(plain, "intervals") <- NULL
gintervals.from_mat(plain, intervals = df[, c("chrom", "start", "end")])
#>   chrom start end t1
#> 1  chr1   100 200  1
#> 2  chr2   200 400  2