Description Usage Arguments Details Author(s) References See Also Examples

View source: R/CumulativeVarPlot.R

The function plots the cumulative variance of the principal components.

1 | ```
CumulativeVarPlot(out, ug = "unguided", ...)
``` |

`out` |
object resulting from |

`ug` |
"guided" or "unguided". Do you want the cumulative variance from guided or unguided PCA plotted. |

`...` |
any other |

This function plots the cumulative variance of the principal components from guided or unguided PCA calculated as (for the unguided case)

*Var_l=\frac{∑_{i=1}^l \var(PC_u)_i}{∑_{i=1}^n \var(PC_u)_i}*

for the *l*th principal component (*l=1,…,n*).

Sarah Reese [email protected]

Reese, S. E., Archer, K. J., Therneau, T. M., Atkinson, E. J., Vachon, C. M., de Andrade, M., Kocher, J. A., and Eckel-Passow, J. E. A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal components analysis. Bioinformatics, (in review).

`gPCA.batchdetect`

, `gDist`

, `PCplot`

1 | ```
# CumulativeVarPlot(out,ug="unguided",col="blue")
``` |

```
```

gPCA documentation built on May 30, 2017, 8:16 a.m.

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