readChangeoDb - Read a Change-O tab-delimited database file

Description

readChangeoDb reads a tab-delimited database file created by a Change-O tool into a data.frame.

Usage

readChangeoDb(file, select = NULL, drop = NULL, seq_upper = TRUE)

Arguments

file
tab-delimited database file output by a Change-O tool.
select
columns to select from database file.
drop
columns to drop from database file.
seq_upper
if TRUE convert sequence columns to upper case; if FALSE do not alter sequence columns. See Value for a list of which columns are effected.

Value

A data.frame of the database file. Columns will be imported as is, except for the following columns which will be explicitly converted into character values:

  • SEQUENCE_ID
  • CLONE
  • SAMPLE

And the following sequence columns which will converted to upper case if seq_upper=TRUE (default).

  • SEQUENCE_INPUT
  • SEQUENCE_VDJ
  • SEQUENCE_IMGT
  • JUNCTION
  • GERMLINE_IMGT
  • GERMLINE_IMGT_D_MASK

Examples

### Not run:
# Read all columns in and convert sequence fields to upper case
# db <- readChangeoDb("changeo.tsv")
# 
# # Subset columns and convert sequence fields to upper case
# db <- readChangeoDb("changeo.tsv", select=c("SEQUENCE_ID", "SEQUENCE_IMGT"))
# 
# # Drop columns and do not alter sequence field case
# db <- readChangeoDb("changeo.tsv", drop=c("D_CALL", "DUPCOUNT"), 
# seq_upper=FALSE)

See also

Wraps read_delim. See writeChangeoDb for writing to Change-O files. See read_rearrangement and write_rearrangement to read and write AIRR-C Standard formatted repertoires.