alakazam (version 0.2.2)

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

See Also

Wraps read.table.

Other file input and output functions: makeTempDir, writeChangeoDb

Examples

# Load example data
file <- system.file("extdata", "ExampleDb.gz", package="alakazam")

# Subset columns and convert sequence fields to upper case
df <- readChangeoDb(file, select=c("SEQUENCE_ID", "SEQUENCE_IMGT"), seq_upper=TRUE)

# Drop columns and do not alter sequence field case
df <- readChangeoDb(file, drop=c("D_CALL", "DUPCOUNT"), seq_upper=FALSE)