fread.osc: Read and return an OSC table.
In charles-plessy/oscR: Read, write and manipulate order-switchable column tables

Description Usage Arguments Details Value Author(s) See Also

Reads an OSC table from a file and returns a data table.

1 2	fread.osc(file, dropIdCoords = FALSE, replaceIdCoords = TRUE, drop.norm = TRUE)

`file`	File name of the OSC table. If its name finishes with `gz`, it will be uncompressed with the `zcat` command.
`dropIdCoords`	`id`, `chrom`, `start.0base`, `end` and `strand` columns.
`replaceIdCoords`	Replaces the contents of the `id` column with a browser-friendly genomic coordinate, and drops the `chrom`, `start.0base`, `end` and `strand` columns.
`drop.norm`	Drops the normalised expression values (any column whose name contains `norm.`). When IDs can be reconstituted from the OSC header and the feature coordinates, the data table can be made lighter by dropping the "id" column with the `replaceIdCoords` option.

This function is still experimental and backwards compatibility may be broken without much notice.

Returns a data table. With OSCTables output by the level1 program, the combiation drop.norm and dropIdCoords will produce a data table that only contains numeric values.

Charles Plessy

data.table, read.osc

charles-plessy/oscR documentation built on May 13, 2019, 3:31 p.m.