Displaying 16 results from an estimated 16 matches for "methylation".
2013 Apr 24
1
R cannot find the path on my mac
...I really don't know why. I have found the path by going to the folder and finding the info about the folder, where the location of this is stated. I copy-paste this into the source command.
The path for the folder is:
When found with the "info about the folder":
/Users/gban/Desktop/Methylation analysis/MethylationDataAnalysis
But I think it should be:
/Users/gban/Desktop/Methylation analysis/MethylationDataAnalysis/1.Normalization_raw_data/
as it is the folder 1.Normalization_raw_data where my data are in.
I have tried both paths but it returns with this message every time:
> sourc...
2011 Jul 27
2
Writing a summary file in R
Hello,
I have an input file:
http://r.789695.n4.nabble.com/file/n3700031/testOut.txt testOut.txt
where col 1 is chromosome, column2 is start of region, column 3 is end of
region, column 4 and 5 is base position, column 6 is total reads, column 7
is methylation data, and column 8 is the strand.
I would like a summary output file such as:
http://r.789695.n4.nabble.com/file/n3700031/out.summary.txt out.summary.txt
where column 1 is chromosome, column 2 is start of region, column 3 is end
of region, column 4 is total reads in general, column 5 is total...
2011 Aug 10
2
Loops for repetitive task
...ied in a general sense.
################################Code###############################
chr2.data<-read.table(file="chr2.out.txt", header=F)
colnames(chr2.data)<-c("chr","start","end","base1","base2","totalreads","methylation","strand")
splc2<-split(chr2.data, paste(chr2.data$chr))
chr2.df<-as.data.frame(t(sapply(splc2, function(x)
list(TR=NROW(x[['totalreads']]), RG1=sum(x[['totalreads']]>=1),
percent=(NROW(x[['totalreads']]>=1)/sum(x[['totalreads']]))))))
c...
2013 Jul 20
1
BH correction with p.adjust
...equation for this was:
pBH = p*n/i
where p is the original p value, n is the number of tests and i is the rank of the p value. However when I try and recreate the corrected p from my most significant value it does not match up to the one computed by the method p.adjust:
> setwd("C:/work/Methylation/IMA/GM/siteLists")
>
> hypTable <- read.delim("hypernormal vs others.txt")
> pList <- hypTable$p
> names(pList) <- hypTable$site
>
> adjusted <- p.adjust(pList, method="BH")
> adjusted[1]
cg27433479
0.05030589
>
> pList[1]*nrow(hy...
2017 Jun 09
1
efetch result not in character format
...a query search in
character format. When I use efetch, the accession number isn't in a
character format, and I'm not sure if the number is accurate, because I get
the error:
Error in file.exists(destfile) : object 'destfile' not found
This is what I tried:
UIDs<-esearch( "Methylation" )
accession_numbers = efetch(UIDs, rettype = "acc")
How do I obtain only the accession number and is the number accruate?
Thank you
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2018 Mar 05
0
data analysis for partial two-by-two factorial design
...analyze the data.
There are nine dishes of cells. Three replicates for each treatment combination. So randomly select three dishes for no drug A/no drug B treatment, a second three dishes for drug A only, then last three dishes to add both A and B drugs. After drug treatments, they measure DNA methylation and genes or gene expression as outcome or response variables(two differnet types of response variables).
My boss might want to find out net effect of drug B, but I think we can not exclude the confounding effect of drugA. For example, it is possible that drug B has no effect, only has effect when...
2004 Oct 20
1
Drawing multiple line plots
Hi All:
Greetings, and best wishes from the festive times here at Kolkata, India -- the time of Durga Puja celebrations.
I seek your advice as I try plotting lines for my data. The problem:
I have created a dataframe that looks like this (name: myFrame):
lowest second third fourth highest significance
INAS 0.107 0.115 0.123 0.115 0.166 0.000
MMA 0.091 0.107 0.115
2018 Mar 05
5
data analysis for partial two-by-two factorial design
David:
I believe your response on SO is incorrect. This is a standard OFAT (one
factor at a time) design, so that assuming additivity (no interactions),
the effects of drugA and drugB can be determined via the model you rejected:
For example, if baseline control (no drugs) has a response of 0, drugA has
an effect of 1, drugB has an effect of 2, and the effects are additive,
with no noise we
2018 Mar 12
0
pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks
Hello all,
I would like to introduce our group's new bioinformatics package to you: pathfindR <https://cran.r-project.org/package=pathfindR>
This tool is designed to improve pathway enrichment analysis by firstly identifying active subnetworksin differential expression/methylation data using a protein-protein interaction network. It then performs pathway enrichment analysis (Over-Representation Analysis). By utilizing the interaction information, the tool identifies most of the involved pathways.
pathfindR also creates pathway diagrams with the involved genes colored by chan...
2011 Oct 28
0
Help with increasing the speed of script
...;),
header=F)
colnames(chrData[[i]])<-c("chr","start","end","tot","methy")
splc[[i]]<-split(data[[i]], paste(data[[i]]$chr, data[[i]]$start,
data[[i]]$end))
df.summ[[i]]<-as.data.frame(t(sapply(splc[[i]], function(x)
summary(1-x$methylation))))
cat("finished reading",paste('chr',i),date(),"\n")
}
#################################################
1) I'll start off first with perhaps the easier question. The above script
is a portion of r code that I run from batch through a pipeline. I've
decided...
2007 Mar 20
0
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2018 Mar 12
0
pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks
Hello all,
I would like to introduce our group's new bioinformatics package to you: pathfindR <https://cran.r-project.org/package=pathfindR>
This tool is designed to improve pathway enrichment analysis by firstly identifying active subnetworksin differential expression/methylation data using a protein-protein interaction network. It then performs pathway enrichment analysis (Over-Representation Analysis). By utilizing the interaction information, the tool identifies most of the involved pathways.
pathfindR also creates pathway diagrams with the involved genes colored by chan...
2007 May 23
2
problem with read.table
Dear all,
I try to use read.table to get the data from a tab delimited file, and some
of the data is shown below:
3185 heterogeneous nuclear ribonucleoprotein F
3187 heterogeneous nuclear ribonucleoprotein H1 (H)
3188 heterogeneous nuclear ribonucleoprotein H2 (H')
3189 heterogeneous nuclear ribonucleoprotein H3 (2H9)
3190 heterogeneous nuclear ribonucleoprotein K ///
2006 May 17
2
Justifying R to anti open-source management
Hi
I apologise for this question as it really must be a FAQ. Unfortunately,
I can't find the answer and I'm tired of looking at endless google results
A colleague of mine works for a state government department that has a
policy against open source software or software tainted by open
source. Other government departments in the same state use R but this
particular department is driven
2009 Dec 17
2
some help regarding combining columns from different files
Dear all,
Here is my code which am using to combine 5th column from different data
sets.
Here is the function to do my job
genesymbol.append.file <-NULL
gene.column <- NULL
readGeneSymbol <- function(files,genesymbol.column=5){
for(i in fnames){
temp <- read.table(fnames,header=T,sep="\t",stringsAsFactors=F,quote="\"")
2012 May 20
1
CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week
New packages
------------
* bisectr (0.0.2)
Maintainer: Winston Chang
Author(s): Winston Chang <winston at stdout.org>
License: GPL-2
http://crantastic.org/packages/bisectr
Tools to find bad commits with git bisect
* CUMP (1.0)
Maintainer: Xuan Liu
Author(s): Xuan Liu <liuxuan at bu.edu> and Qiong Yang <qyang at bu.edu>