R Onto-Tools suite iPathwayGuide

From iPathwayGuide, our pathway analysis approach is based on novel Impact Analysis method. This paper, published in Genome Research, explains the underlying analytic method and also demonstrates how Impact Analysis avoids costly false positive results as generated by other methods such as Over-Representation Analysis. The tool is also available from ROntoTools

advanced r wiki

From hadley, who is like a god in R.
The discussion of environment is really helpful. I am aware of other excellent resources, but still did not get it from there. 

graphic output for non-pdf file under unix without X11

bitmap('convergence%03d.png', height=11, width=8, res=600);
plot(post[, selectNode2Plot])
dev.off();

Created by Pretty R at inside-R.org

sas datasets IO with R

R code lines below are run without SAS installed.

Quickly insert all sheet names in cells with VBA

from here:

If you want to inset all sheet names in cells, VBA macro is a good choice.
Step 1: Hold down the Alt + F11 keys in Excel, and it opens the Microsoft Visual Basic for Applications window.
Step 2: Click Insert > Module, and paste the following macro in the Module Window.
VBA for inserting all worksheets' names in cells:

Sub SheetNames()
Columns(1).Insert
For i = 1 To Sheets.Count
Cells(i, 1) = Sheets(i).Name
Next i
End Sub

seriation

Seriation, also the name for an R package 

is to arrange all objects in a set in a linear order given available data and some loss or merit function in order to reveal structural information. Together with cluster analysis and variable selection, seriation is an important problem in the field of combinatorial data analysis

This post discussed the application of seriation on plotting binary matrices, together with other clustering algorithms.

Prioritizing GWAS Results

This review paper mentioned 3 analytic methods to prioritizing GWAS results (for follow-up studies):

• Meta-analysis seeks to pool information from multiple GWAS to increase the chances of finding true positives among the false positives and provides a way to combine associations across GWAS, even when the original data are unavailable.

• Testing for epistasis within a single GWAS study can identify the stronger results that are revealed when genes interact.

• Pathway analysis of GWAS results is used to prioritize genes and pathways within a biological context. Following a GWAS, association results can be assigned to pathways and tested in aggregate with computational tools and pathway databases.

a tutorial for ggplot2, comprehensive and concise

here

The default plot function from glmnet is quite basic and plain. The following function tries to improve the plots

#this function is to achieve the same purpose of plot.glmnet()
#with the following enhancement:

# 1) show variable number instead of column number
# 2) show the value of lambda that gives smallest cross validation error with a solid line
# 3) show the largest lambda such that the error is within 1 se of the minimal cross validation error with a dashed line
 
#input variables: a glmnet object from glmnet(), a cv. glmnet object from cv.glmnet(), and a possible plot title
 

rjags conflicts with igraph

#Start a new R session with --vanilla;
 
library(igraph) # version 0.6-2
n1 <- read.graph ('network.txt', format="ncol", directed=F, name=T); 

a1 <- get.adjacency="" n1="" pre="" type="both">
if (is.connected(n1, mode="weak")){ 
    #do something 
} 
 
library(rjags) #version 3.5
data(LINE)
LINE$recompile() #example analysis included in rjags
 
#Start a new R session with --vanilla, and the following line runs smoothly;
 
library(rjags) #version 3.5
data(LINE)
LINE$recompile()

Created by Pretty R at inside-R.org

inline rjags

from here

igraph tutorial

http://horicky.blogspot.com/2012/04/basic-graph-analytics-using-igraph.html
http://igraph.sourceforge.net/igraphbook/
leaves = V(g)[degree(g, mode="out")==0]

from here:

The methods under consideration included observed case MMRM, per protocol visits MMRM, interval last observation carried forward (LOCF) MMRM, and a hybrid of the per protocol visits and interval LOCF MMRM approaches.Simulation results reveal that the method that best controls the type I error rate is the per protocol visits method.

HapMap 3: more people ~ more genetic variation

from here.
Centre d’Etude du Polymorphisme Humain collected in Utah, USA, with ancestry from northern and western Europe (CEU)
Han Chinese in Beijing, China (CHB)
Japanese in Tokyo, Japan (JPT)
Yoruba in Ibadan, Nigeria (YRI)
African ancestry in the southwestern USA (ASW)
Chinese in metropolitan Denver, Colorado, USA (CHD)
Gujarati Indians in Houston, Texas, USA (GIH)
Luhya in Webuye, Kenya (LWK)
Maasai in Kinyawa, Kenya (MKK)
Mexican ancestry in Los Angeles, California, USA (MXL)
Tuscans in Italy (Toscani in Italia, TSI)
So memorize some of those abbreviations! One particular difference across these populations is that some are parent-offspring trios, and some are not. So the CEU sample are trios, while the TSI are not.

R factor

Convert a character vector into 1:xxx

f1 <- class="st" span="span" unlist="unlist">strsplit("cabbage", split=""))

as.numeric(unclass(factor(f1))) # levels are coded 1:n according to their alphabetical order

as.numeric(unclass(factor(f1, levels=unique(f1)))) # levels are coded 1:n according to their first appearence

ggplot2 trick

• aes_string
• when facet_wrap does not work:

Here's some code from Hadley's book that assumes you've created ggplot objects a, b, and c. It puts a in the top row, with b and c in the bottom row.

grid.newpage()
pushViewport(viewport(layout=grid.layout(2,2)))
vplayout<-function(x,y){
    viewport(layout.pos.row=x,layout.pos.col=y) 

}

print(a,vp=vplayout(1,1:2))
print(b,vp=vplayout(2,1))
print(c,vp=vplayout(2,2))

Created by Pretty R at inside-R.org

• different line style from geo_smooth in different facet_wrap

p1 <- ggplot(ds2, aes(x=visit, y=change))+ geom_point(shape=1, 

aes(color=treat), position=position_jitter(width=0.4,height=0)) 

+ facet_grid(snp~race)+ opts(title = 'rsxxxx')
 
p1 <- p1 + geom_smooth(data=subset(ds2, race == 'CA'), method='lm', 

se=F, color='blue', linetype = ifelse(pValues[pValues$'dbsnprsid' 

== 'rsxxxx', 'slope1_p'] < 0.05 ,"longdash", "solid" ))
 

Created by Pretty R at inside-R.org

•  background color in the plotting area

+ theme_grey() - the default theme, with a grey background
+ theme_bw() - a theme with a white background 

Created by Pretty R at inside-R.org

inverse gamma and gamma distribution

here

sas dataset merging

from sas 9.1.3 language reference

mean corr is equal to sample corr

at least for independent pairs. For prove see here.

winbugs notes

1. in winbugs script, the file path cannot be longer than 108 characters; otherwise, there will be an incompatible copy error message
2. from R2winbugs, even seed is set to NULL (the default), chains from winbugs are identical given identical initial values and data sets. Guess winbugs figure out a fixed seed based upon these input.
3.  a good reference for specify covariance matrix prior for multivariate normal. However, there are comments that promote scaled inverse Wishart instead of inverse Wishart as the prior for precision. An illustration against inverse Wishart can be found here. 
4. scaled inversed wishart recommended by Gelman. Need set df = K+ 1 to make individual correlation coefficient uniform on [-1,1], where K is the dimension of the Cov matrix (although df=K is the minimum allowed df). A winbugs implementation can be found here: it actually scales the y variable, which indirectly scale the covariance matrix.
5. From winbugs manual: "Note that WinBUGS simulates each node in turn: this can make convergence very slow and the program very inefficient for models with strongly related parameters, such as hidden-Markov and other time series structures." Thus, strongly related parameters should be put into one multivariate node.
6. For parameters for repeated measures, reference coding of effect (treating a visit as a reference, and other visits as deviation from the reference) seems to perform worse than cell mean effect coding (just a separate parameter for each visit). This is probably because the later gives rise to a orthogonal design matrix. 
7. to convert a object (eg. wb) returned from function 'bugs' in R2WinBUGS (codaPkg=FALSE ), we can use coda1 <- as.mcmc.list(wb). See the documentation of 'codaPkg' for more details.
8. openbugs is not necessary better than winbugs in perfomance and scalibility. 
1. openbugs has no automatic graphic output, which is good when we are not worried about convergence and when we run it through many cycles (eg. in simulations)
2. openbugs runs in unix.
9. Missing values are treated as a stochastic node and effectively 'imputed' by winbugs. However, such imputed data will not inflate precision (since they are not treated as data, but parameters by winbugs). It is possible to take this imputation procedure out: run multiple imputation and feed full data into winbugs to mimic the internal imputation procedure implemented by winbugs.We will have additional data from imputation (hence increase precision), but the variation among different imputed datasets, which will be fed one by one and posterior distributions merged, may compensate for the increased precision.
10. A good resource for DIC