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; ifFALSE
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. See read_rearrangement and write_rearrangement to read and write AIRR-C Standard formatted repertoires.