alakazam (version 1.3.0)

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)

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

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.

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

if (FALSE) {
    # 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)
}