massi_select {massiR} | R Documentation

## massi_select

### 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)

[Package massiR version 1.18.0 Index]