massi_select: massi_select

In SamBuckberry/bioc_massiR-release: massiR: MicroArray Sample Sex Identifier

Description

This function selects the y chromosome probe data for each sample.

Usage

massi_select(expression_data, y_probes, threshold = 3)

Arguments

expression_data	The expression.data item contains normalized array expression data for all samples. This can be a data.frame with sample names as columns and probe id's as row names. This argument also allows the specification of an ExpressionSet object.
y_probes	A data.frame of probe id's in one column that match y chromosome genes for the array platform. massiR includes probes for several Illumina and Affymetrix platforms. Details on using these probes are included in the vignette and the y.probes manual.
threshold	The threshold value corresponds to probe variation quantiles. This option allows the selection of the most variable probes. Deciding on a probe threshold value should be informed by viewing the plot generated by the massi_y_plot function. Threshold must be an integer "1", "2", "3", or "4". A threshold of "1" will select all y chromosome probes matching the id's in y.probes, Thresholds of "2", "3" and "4" will select probes with a CV in the top 75%, 50% and 25% respectively. The aim here is to remove probes with little to no variance across the samples. Default = 3.

Value

A data.frame containing the subset of y chromosome probe values for each sample.

Author(s)

Sam Buckberry

See Also

massi_y, massi_cluster, massi_y_plot, massi_dip, massi_cluster_plot

Examples

data(massi.test.dataset, massi.test.probes)

massi_select(expression_data=massi.test.dataset, y_probes=massi.test.probes)

SamBuckberry/bioc_massiR-release documentation built on May 9, 2019, 12:22 p.m.