preparePlotgardener

This function allows to obtain a dataframe that can be used with plotgardener's plotHicTriangle, plotHicRectangle, plotHicSquare. It is equivalent to plotgardener's readHic function.

Usage

preparePlotgardener(
  hicList = NULL,
  ctrlHicList = NULL,
  submatrices = NULL,
  submatrix.name = NULL,
  diffFun = "log2ratio",
  which_chrom = NULL,
  which_range = NULL
)

Arguments

hicList

hicList from which to extract data

ctrlHicList

hicList to use as control for a differential analysis.

submatrices

list of submatrices.

submatrix.name

name of submatrix to focus on. use names(submatrices). If submatrices is not NULL, this argument must not be NULL.

diffFun

The function used to compute differential between counts column of hicList and ctrlHicList. If the argument is a character, possible choices are:

• "-", "substract" or "substraction" apply a substraction (Default)

• "/" or "ratio" apply a ratio

• "log2","log2-","log2/" or "log2ratio" apply a log2 on ratio

• other apply a log2 on 1+ratio

which_chrom

a combination of chromsome names use names(hicList) to see the possible names.

which_range

a GRanges object or a string of type "chr1:1-100". see StrToGranges().

Value

funcions returns a data.frame with 3 columns: chrom, altchrom and counts. chrom being bin names of rows, altchrom being bin names of columns and counts being the counts. see also strawr::straw() & plotgardener::readHic()

Examples

data(HiC_Ctrl.cmx_lst)
data(HiC_HS.cmx_lst)
preparePlotgardener(
  hicList = HiC_HS.cmx_lst,
  ctrlHicList = HiC_Ctrl.cmx_lst,
  which_chrom = "2L_2L",
  diffFun = "substract")|> head()
#>   chrom altchrom counts
#> 1 0e+00    0e+00   5724
#> 2 0e+00    1e+05   3695
#> 3 1e+05    1e+05   2747
#> 4 0e+00    2e+05    398
#> 5 1e+05    2e+05   6324
#> 6 2e+05    2e+05   5613