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

readChangeoDb {alakazam} | R Documentation

## 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.

### 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)

[Package alakazam version 0.3.0 Index]