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

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

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

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.

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)

## End(Not run)

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.