ExtractProjection {rgsepd} | R Documentation

## ExtractProjection

### Description

This function takes a completed GSEPD object with sample data, and a set of gene identifiers and produces the projection of sample expression in the sub-space.

### Usage

    ExtractProjection(GSEPD, txids, DRAWING=FALSE, GN=c(1,2), PRINTING=FALSE, plotTitle="")

### Arguments

`GSEPD` | The GSEPD parameter object. Must be post-Process.
`txids` | The transcript IDs, generally REFSEQ identifiers corresponding to rows of the counts table for this a projection is desired. In normal usage these are based on a GO Term.
`DRAWING` | Boolean flag to draw a plot of the projection.
`GN` | The gene numbers: which items of the 'txids' list are to be drawn. Only the first two are used. If Drawing=FALSE, this parameter is irrelevant.
`PRINTING` | Boolean flag to print some debug information.
`plotTitle` | A name for this set of genes, serves as the plot's main title.

### Details

Primary gene set projection tool. This function calculates the vector projection and axis in a N-dimensional space of gene expression for a set of samples. When DRAWING=TRUE you will get some diagrams of the expression normalized counts.

### Value

Returns a list object with four values for each sample.

`alpha` | Distance along the axis from group1 to group2, generally 0-1, as in percent. Samples within group 1 should average zero, and samples in group 2 should average one.
`beta` | Distance from the samples to the axis. This is a measure of goodness of fit, when the value is zero it means the sample is a linear interpolation between the comparison groups. When the value is high, the sample is not along the n-dimensional axis.
`gamma1` | Distance from the samples to the center of group1
`gamma2` | Distance from the samples to the center of group2
`Validity.Score` | A score, 0% through 100%, of the segregation validity for this gene set among the two sample test groups.
`Validity.P` | The validity score's associated p-value, empirically calculated chance of a random sample assignment creating such a strong score.

### Examples

      data("IlluminaBodymap")
      data("IlluminaBodymapMeta")
      set.seed(1000) #fixed randomness
      isoform_ids <- Name_to_RefSeq(c("HIF1A","EGFR","MYH7","CD33","BRCA2"))
      rows_of_interest <- unique( c( isoform_ids ,
                                     sample(rownames(IlluminaBodymap),
                                            size=2000,replace=FALSE)))
      G <- GSEPD_INIT(Output_Folder="OUT",
                    finalCounts=round(IlluminaBodymap[rows_of_interest , ]),
                    sampleMeta=IlluminaBodymapMeta,
                    COLORS=c("green","black","red"))

      G <- GSEPD_ChangeConditions( G, c("A","B")) #set testing groups first!
      G <- GSEPD_Process( G ) #have to have processed results to plot them

       # looking at genes 2 and 3 will show us a view in dimensions "EGFR" and "MYH7"
       # and an axis through five dimensional space.
      ExtractProjection(GSEPD=G, txids=isoform_ids,
        DRAWING=TRUE, PRINTING=TRUE, GN=c(2,3))

[Package rgsepd version 1.16.0 Index]