Convert contact matrix

Source: R/writer.R

This function can covert a contact matrix (x, y, counts) format into a short with score format.

convertJuicer(contactMatrix, chr1, chr2)

Arguments

contactMatrix

A contact matrix, the first column is the first chromosome location, and second column is the second chromosome location, the third column is count number
chr1

The first chromosome name. For example, 1 or 'chr1'.
chr2

The second chromosome name. For example, 1 or 'chr1'

Value

A data.frame has 9 columns, and it can be used directly by juicer Pre.

See also

writeJuicer.

Examples


## Create a random contact matrix

contactMatrix <- structure(
c(0L, 0L, 50L, 0L, 50L, 100L, 0L, 50L, 50L, 100L, 100L,
100L, 526L, 123L, 499L, 36L, 213L, 562L), .Dim = c(6L, 3L),
.Dimnames = list(NULL, c('x', 'y', 'counts')))

contactMatrix
#>        x   y counts
#> [1,]   0   0    526
#> [2,]   0  50    123
#> [3,]  50  50    499
#> [4,]   0 100     36
#> [5,]  50 100    213
#> [6,] 100 100    562

## chromosomes names

chr1 = 'chr1'
chr2 = 'chr2'

## Convert to hic
df = convertJuicer(contactMatrix, chr1, chr2)
head(df)
#>   str1 chr1 pos1 frag1 str2 chr2 pos2 frag2 score
#> 1    0 chr1    0     0    0 chr2    0     1   526
#> 2    0 chr1    0     0    0 chr2   50     1   123
#> 3    0 chr1   50     0    0 chr2   50     1   499
#> 4    0 chr1    0     0    0 chr2  100     1    36
#> 5    0 chr1   50     0    0 chr2  100     1   213
#> 6    0 chr1  100     0    0 chr2  100     1   562