return_corrected_umi: Return corrected UMI sequences

In cziegenhain/UMIcountR: tools for spike-in UMI analysis

Return corrected UMI sequences

Description

return_corrected_umi performs error correction on an input vector of raw UMI sequences.

error_correct_known performs error correction on an input vector of raw sequences and a list of expected sequences.

Usage

return_corrected_umi(
  umi_input,
  editham = 1,
  collapse_mode = NULL,
  ngram_split = NULL
)

error_correct_known(obs_seqs, known_seqs, editham = 1, set_NA_nonmatch = FALSE)

Arguments

umi_input	input character vector of uncorrected UMI sequences
editham	edit distance (hamming) used for collapse, Default: 1
collapse_mode	collapse mode to use, Default: adjacency
obs_seqs	input character vector of uncorrected observed sequences
known_seqs	input character vector of expected known sequences
set_NA_nonmatch	set sequences that do not match to known list after error correction to NA?

Details

For a description of implemented collapse algorithms, please refer to Ziegenhain, Hendriks et al., 2021.

NA

Value

returns a vector of error-corrected UMIs with same length as input sequences. Implemented collapse algorithms: "adjacency","adjacency_directional","adjacency_singleton","cluster"

returns a vector of error-corrected sequences with same length as input sequences.

See Also

data.table-package

data.table-package

Examples

## Not run: 
return_corrected_umi(UX_strings, editham = 1, collapse_mode = "adjacency")

## End(Not run)
## Not run: 
error_correct_known(in_strings, known_strings, editham = 1)

## End(Not run)

cziegenhain/UMIcountR documentation built on May 30, 2022, 5:38 p.m.