Add back chr, start, end of bins missing from cells

Often we filter read bins based on various criteria, or tools we use might drop bins of read/state data. This function will put missing bins back into a dataframe for cells.

Usage

add_missing_bins_for_cells(
  state_df,
  version = c("hg19", "hg38"),
  bin_size = 5e+05,
  cell_metadata_cols = c(),
  input_chroms_only = TRUE
)

Arguments

state_df

the dataframe/tibble to insert the missing bins into

version

which genome version you are using. Default "hg19", or select "hg38"

bin_size

size of bins that should be there.

cell_metadata_cols

vector of columns to carry through to inferred bins

input_chroms_only

bool. Only insert bins for chromosomes in the input state dataframe. I.e., if you've filtered X or Y, don't add bins for X or Y. Setting to FALSE adds bins for entire genome. Default: TRUE

Value

input dataframe with extra bins for each cells that were missing.

Details

Basic operation will result in NAs for every column except cell_id, chr, start, end for the newly added bins. But you can also carry over cell metadata by specifying which columns to keep for the inferred bins. This should be cell level data.