GuangchuangYu

No update since 2014.

## Access date: 2017-01-04
$ svn log -q |grep 'z.li'
r87229 | z.li | 2014-03-08 12:13:28 +0800 (Sat, 08 Mar 2014)
r85532 | z.li | 2014-01-15 13:00:43 +0800 (Wed, 15 Jan 2014)
r85454 | z.li | 2014-01-12 13:57:16 +0800 (Sun, 12 Jan 2014)
r72578 | z.li | 2013-01-16 15:11:20 +0800 (Wed, 16 Jan 2013)
r72577 | z.li | 2013-01-16 13:43:05 +0800 (Wed, 16 Jan 2013)

GuangchuangYu

f <- function(a, b) function(y) a * y * log(y, base=10) -1/b * exp(-(b*y - b/exp(1))^4)


y <- seq(0, 1, length.out=100)
cols = colorspace::rainbow_hcl(5)
d1 <- data.frame(x = f(3, 30)(y),   y=y, color=cols[1])
d2 <- data.frame(x = f(2.8, 33)(y),   y=y, color=cols[2])
d3 <- data.frame(x = f(2.5, 36)(y), y=y, color=cols[3])
d4 <- data.frame(x = f(2.2, 40)(y), y=y, color=cols[4])
d5 <- data.frame(x = f(2, 50)(y),   y=y, color=cols[5])

GuangchuangYu

require(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
library(ChIPseeker)
library(GenomicRanges)
# Hack chipseeker function to add annotaiton
getGenomicAnnoStat <- function(peakAnno) {
    if ( class(peakAnno) == "GRanges" )
        peakAnno <- as.data.frame(peakAnno)
    anno <- peakAnno$annotation
    ## anno <- sub(" \\(.+", "", anno)

GuangchuangYu

scheme

https://www.shido.info/lisp/idx_scm_e.html http://deathking.github.io/yast-cn/index.html

sicp

https://github.com/jiacai2050/sicp

GuangchuangYu

## http://ygc.name/2012/05/29/t-test/


p1 <- rnorm(1000)
p2 <- rnorm(1000, sd=3)

hist(p2, col="green", xlab="", main="")
hist(p1, col="red", add=T)

legend(legend=c("sd=1", "sd=3"), fill=c("green", "red"), x="topright")

GuangchuangYu

x <- read.csv("/Volumes/YGC/Researches/ARCHIVE/Others/AL-1-by-GR.Yan/2D-data-and-analysis-result/2D.csv")
eg <- as.character(x[,1])
require(clusterProfiler)
xx <- enrichGO(eg, ont="BP")
gg <- xx@geneInCategory
names(gg) <- clusterProfiler:::TERM2NAME.BP(names(gg))

g <- gg[1:4]
require(gplots)
vm <- venn(g)

GuangchuangYu

# http://ygc.name/2012/04/29/bootstrap-for-enrichment-analysis/

goboot <- cmpfun(function(goid,
                          sampleSize,
                          nboot=1000) {
    ratio <- rep(0, nboot)

    allgene <- unique(mappedkeys(org.Hs.egGO))
    allgeneInCategory <- unique(get(goid, org.Hs.egGO2ALLEGS))

GuangchuangYu

set.seed(123)

x <- rnorm(100)
y <- rnorm(100)
points.df <- data.frame(x=x,y=y)

center <- c(0.2, 0.3)
diameter <- 2

d <- apply(points.df, 1, function(x) x-center)

GuangchuangYu

## http://ygc.name/2011/08/02/q-q-plots/

qqplot <- function(y, distribution=qnorm) {
  x <- distribution(ppoints(y))
  plot(x, sort(y),
       xlab="Theoretical Quantiles",
       ylab="Sample Quantiles",
       main="Normal Q-Q Plot"
       )
  lines(y,y)

GuangchuangYu

fibonacci <- function(n) {
    u <- (1+sqrt(5))/2
    (u^n - (1-u)^n) / sqrt(5)
}