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.