a question about sort and BH

Hi,

I have two questions want to ask.

1. If I have a matrix like this, and I want to figure out the rows whose
value in the 3rd column are less than 0.05. How can I do it with R.
hsa-let-7a--MBTD1 ? ?0.528239197 ? ?2.41E-05
hsa-let-7a--APOBEC1 ? ?0.507869409 ? ?5.51E-05
hsa-let-7a--PAPOLA ? ?0.470451884 ? ?0.000221774
hsa-let-7a--NF2 ? ?0.469280186 ? ?0.000231065
hsa-let-7a--SLC17A5 ? ?0.454597978 ? ?0.000381713
hsa-let-7a--THOC2 ? ?0.447714054 ? ?0.000479322
hsa-let-7a--SMG7 ? ?0.444972282 ? ?0.000524129

2. I got the p.adjust.R from R source. In the method "BH", I am not clear
with the code:
? ? ? ? ? i <- lp:1L

? ? ? ? ? o <- order(p, decreasing = TRUE)
? ? ? ? ? ro <- order(o)
? ? ? ? ? pmin(1, cummin( n / i * p[o] ))[ro]

How to explain the first and the fourth row.
====================p.adjust.R=======================================
p.adjust.methods <-
? ?c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")
p.adjust <- function(p, method = p.adjust.methods, n = length(p))
{
? ?## Methods 'Hommel', 'BH', 'BY' and speed improvements contributed by
? ?## Gordon Smyth <smyth at wehi.edu.au>.
? ?method <- match.arg(method)
? ?if(method == "fdr") method <- "BH" # back compatibility
? ?nm <- names(p)
? ?p <- as.numeric(p); names(p) <- nm
? ?p0 <- p
? ?if(all(nna <- !is.na(p))) nna <- TRUE
? ?p <- p[nna]
? ?lp <- length(p)
? ?stopifnot(n >= lp)
? ?if (n <= 1) return(p0)
? ?if (n == 2 && method == "hommel") method <- "hochberg"
? ?p0[nna] <-
?switch(method,
? ? ? ?bonferroni = pmin(1, n * p),
? ? ? ?holm = {
? ? i <- seq_len(lp)
? ? o <- order(p)
? ? ro <- order(o)
? ? pmin(1, cummax( (n - i + 1L) * p[o] ))[ro]
? ? ? ?},
? ? ? ?hommel = { ## needs n-1 >= 2 in for() below
? ? if(n > lp) p <- c(p, rep.int(1, n-lp))
? ? i <- seq_len(n)
? ? o <- order(p)
? ? p <- p[o]
? ? ro <- order(o)
? ? q <- pa <- rep.int( min(n*p/i), n)
? ? for (j in (n-1):2) {
? ? ? ? ij <- seq_len(n-j+1)
? ? ? ? i2 <- (n-j+2):n
? ? ? ? q1 <- min(j*p[i2]/(2:j))
? ? ? ? q[ij] <- pmin(j*p[ij], q1)
? ? ? ? q[i2] <- q[n-j+1]
? ? ? ? pa <- pmax(pa,q)
? ? }
? ? pmax(pa,p)[if(lp < n) ro[1:lp] else ro]
? ? ? ?},
? ? ? ?hochberg = {
? ? i <- lp:1L
? ? o <- order(p, decreasing = TRUE)
? ? ro <- order(o)
? ? pmin(1, cummin( (n - i + 1L) * p[o] ))[ro]
? ? ? ?},
? ? ? ?BH = {
? ? i <- lp:1L
? ? o <- order(p, decreasing = TRUE)
? ? ro <- order(o)
? ? pmin(1, cummin( n / i * p[o] ))[ro]
? ? ? ?},
? ? ? ?BY = {
? ? i <- lp:1L
? ? o <- order(p, decreasing = TRUE)
? ? ro <- order(o)
? ? q <- sum(1L/(1L:n))
? ? pmin(1, cummin(q * n / i * p[o]))[ro]
? ? ? ?},
? ? ? ?none = p)
? ?p0
}
============================================================


I wrote a code to do my work in BH correction like the following:

rm(list=ls())
a<-read.csv("test.txt",sep="\t",header=F,quote="")
b<-a[order(a[,3],decreasing=TRUE),]
c<-p.adjust(b[,3],method="BH")
b[,4]<-c
write.table(b,"zz.txt",sep="\t")

Is that right? Thanks for all.

Jiang

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