qqnorm-methods {DEDS} | R Documentation |

The function `qqnorm.DEDS`

produces normal Quantile-Quantile
plots of statistics for `DEDS-class`

objects. The points
corresponding to genes with DEDS q- or adjusted p-values less than
a user defined threshold are highlighted.

## S3 method for class 'DEDS': qqnorm(y, subset=c(1:nrow(y$stats)), xlab = "Quantiles of standard normal", thresh = 0.05, col = palette(), pch, ...)

`y` |
An object of `DEDS` , produced by
`deds.stat.linkC` or `deds.stat` . |

`subset` |
A numeric vector indicating the subset of points to be plotted. |

`xlab` |
A title for the x axis |

`thresh` |
A numeric variable specifying the threshold of significance in differential expression (DE) for q- or p-values of the DEDS object. |

`col` |
A specificatio for the colors to be used for plotting. It should have a length bigger than two. The first is used for points with q- or adjusted p-values smaller than the specified threshould (group I) and the second for points with q- or adjusted p-values bigger than the threshould (group II). |

`pch` |
A specification for the type of points to be used for plotting. It should have a length bigger than two. The first parameter is used for group I genes, and the second for group II genes. |

`...` |
Extra parameters for plotting. |

The function `qqnorm.DEDS`

implements a S3 method of
`qqnorm`

for `DEDS`

. The `DEDS`

class is a simple list-based class to store DEDS results and
`qqnorm.DEDS`

is used for a DEDS object that is created by
functions `deds.stat`

, `deds.stat.linkC`

. The
list contains a "stat" component, which stores statistics from
various statistical tests. The function `qqnorm.DEDS`

extracts the
"stat" component and produces a normal QQ plot for each type of
statistics. `qqnorm.DEDS`

as a default highlights points
(corresponding to genes) with DEDS adjusted p- or q-values less than
a user defined threshold.

For DEDS objects that are created by the function
`deds.pval`

, the "stat" matrix consists of unadjusted
p-values from different statistical models. For graphical display of
these p values, the user can use `hist.DEDS`

and
`pairs.DEDS`

.

Yuanyuan Xiao, yxiao@itsa.ucsf.edu,

Jean Yee Hwa Yang, jean@biostat.ucsf.edu.

`deds.stat`

, `deds.pval`

,
`deds.stat.linkC`

, `hist.DEDS`

,
`qqnorm.DEDS`

X <- matrix(rnorm(1000,0,0.5), nc=10) L <- rep(0:1,c(5,5)) # genes 1-10 are differentially expressed X[1:10,6:10]<-X[1:10,6:10]+1 # DEDS summarizing t, fc and sam d <- deds.stat.linkC(X, L, B=200) # qqnorm for t, fc and sam qqnorm(d) # change points color qqnorm(d, col=c(2,3)) # change points type qqnorm(d, pch=c(1,2))

[Package *DEDS* version 1.0.3 Index]