getSvs: Do SVA on matrix stored in database

In leekgroup/derfinder: Differential expression analysis of RNA-seq data at base-pair resolution

Description

Performs surrogate variable analysis on a matrix, usually base-pair by sample coverage, so the surrogate variables can be adjusted for in later analysis steps. SVA is meant to provide a method to adjust for unknown confounders.

Usage

getSvs(dbfile, tablename, group, chunksize = 1e+05, colsubset = c(-1))

Arguments

dbfile	Name/location (as character string) of database (usually ".db") file containing nucleotide by sample coverage.
tablename	Name of the table the database contains
group	a 0/1 vector grouping the samples (columns) in the database.
chunksize	How many rows of the database should be processed at a time?
colsubset	Optional vector of column indices of the input file that denote samples you wish to include in analysis. Should NEVER include 1 (genomic position).

Value

An object of class sva - see help files for sva.

Author(s)

Jeff Leek

leekgroup/derfinder documentation built on May 20, 2019, 11:30 p.m.