beadcount: Creates matrix of beacounts from minfi data.

In schalkwyk/wateRmelon: Illumina DNA methylation array normalization and metrics

Creates matrix of beacounts from minfi data.

Description

Creates matrix of beacounts from data read in using the minfi package. NAs represent probes with beadcount <3. An Extended RG Channel Set is required for this function to work.

Usage

beadcount(x)

Arguments

x	450K methylation data read in using minfi to create an Extended RG Channel Set

Value

A matrix of bead counts with bead counts <3 represented by NA for use in the pfilter function for quality control

Note

The beadcount function is internal to the pfilter function

Author(s)

[e-mail]

References

[1] Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalkwyk LC: A data-driven approach to preprocessing Illumina 450K methylation array data (submitted)

schalkwyk/wateRmelon documentation built on Aug. 13, 2024, 9:52 a.m.