stat.gnames {sma} | R Documentation |
Lists genes and corresponding statistics in decreasing order of the
statistics. This function applies to any type of statistic, including
log ratios, one and two-sample t-statistics, and F-statistics. Missing
values are ignored, as in sort(..., na.last=NA)
.
stat.gnames(x, gnames, crit=0.05)
x |
a numeric vector containing the statistics for each gene. Missing values (NAs) are allowed. |
gnames |
a character vector containing the gene names. |
crit |
specifies the number of genes to be returned. If crit < 1, the crit*100% genes with the largest x values are listed. If crit >= 1, the crit genes with the largest x values are listed. |
List containing the following components
gnames |
gene names sorted in decreasing order of the statistics in x. |
t |
statistics sorted in decreasing order. |
Yee Hwa Yang, yeehwa@stat.berkeley.edu
Sandrine Dudoit, sandrine@stat.berkeley.edu
## Calculating log ratio and performing a t test. data(MouseArray) ## mouse.setup <- init.grid() ## mouse.data <- init.data() ## see \emph{init.data} mouse.lratio <- stat.ma(mouse.data, mouse.setup) cl <- c(rep(1,3), rep(2,3)) mouse.t2 <- stat.t2(mouse.lratio, cl) ## Looking at gene names ## Finding the top 10 t-statistics stat.gnames(abs(mouse.t2$t), mouse.gnames, crit=10) ## Finding the top 1 stat.gnames(abs(mouse.t2$t), mouse.gnames, crit=0.01) ## Finding the 10 extreme M values in the first slide stat.gnames(abs(mouse.lratio$M[, 1]), mouse.gnames, crit=10)