Displaying 20 results from an estimated 700 matches similar to: "average two sets of columns"
2012 Jun 21
2
Simple Question?
Greetings,
I am new to R, but trying to put in the time to learn. I have read the R
manual and several other introductory texts; however, there is nothing like
actually putting it into practice. So here is my problem, and its more of a
learning exercise for myself than anything else, but I'm stuck and getting
extremely frustrated that I can't figure it out.
I'm trying to make a
2010 May 20
5
sort a data.frame
Hello,
I have a dataframe:
dd <- data.frame(b = c("chr2", "chr1", "chr15", "chr13"),
x = c("A", "D", "A", "C"), y = c(8, 3, 9, 9),
z = c(1, 1, 1, 2))
>dd
b x y z
1 chr2 A 8 1
2 chr1 D 3 1
3 chr15 A 9 1
4 chr13 C 9 2
Now I want to sort them according column "b", but only its
2012 Sep 15
2
qplot: plotting precipitation data
Dear list,
I wish to plot chromatin precipitation data: I would like to have a
rectangles (x:end-start, y:peak) but I do not have an idea how to define x
(in terms of qplot syntax) and to choose the correct geom.
mydata is a subset of a larger file.
> mydata
chrom start end peak
1 chr11 5291000 5291926 8
2 chr11 10988025 10988526 7
3 chr11 11767950 11768676 8
4
2008 Feb 04
1
counting identical data in a column
Hi Peter
I have the following data frame with chromosome name, start and end positions:
chrN start end
1 chr1 11122333 11122633
2 chr1 11122333 11122633
3 chr3 11122333 11122633
8 chr3 111273334 111273634
7 chr2 12122334 12122634
4 chr1 21122377 21122677
5 chr2 33122355 33122655
6 chr2 33122355 33122655
I would like to count the positions that have the same start and
2008 Feb 06
4
inserting text lines in a dat frame
Hi Jim
I am trying to prepare a bed file to load as accustom track on the UCSC genome browser.
I have a data frame that looks like the one below.
> x
V1 V2 V3
1 chr1 11255 55
2 chr1 11320 29
3 chr1 11400 45
4 chr2 21680 35
5 chr2 21750 84
6 chr2 21820 29
7 chr2 31890 46
8 chr3 32100 29
9 chr3 52380 29
10 chr3 66450 46
I would like to insert the following 4 lines at the beginning:
2011 Jan 31
1
how to search to value to another table
Hello,
I'm a new R user.
I have two different dummy tables with the variable name tb1 and tb2.
tb1<
v1 v2 v3 v4
"chr1" 22 23 3
"chr1" 36 37 1
"chr1" 54 55 0
"chr1" 77 78 1
"chr2" 80 81 4
"chr2" 85 86 0
"chr2" 99 100 1
2011 Aug 10
2
Loops for repetitive task
Hello,
I have an R script that I use as a template to perform a task for multiple
files (in this case, multiple chromosomes).
What I would like to do is to utilize a simple loop to parse through each
chromosome number so that I don't have to type the same code over and over
again in the R console.
I've tried using:
for(i in 1:22){
etc..
}
and replacing each chromosome number with
2011 Apr 15
1
Whole genome searching of 100bp "D" sequence
Hi,
I was wondering I'm going about this in the correct way. I need to test if
there are coding sequences or exons in hg19 which match a string of 100bp
"D" i.e. [A,G or T]. However I'm getting a strange result.
I get a hit on chr7, using the 100bp search however when I search with 60bp
sequence of "D" I don't get any hits.
library("BSgenome")
2011 Oct 17
2
Histogram for each ID value
I have a dataframe in the general format:
chr1 0.5
chr1 0
chr1 0.75
chr2 0
chr2 0
chr3 1
chr3 1
chr3 0.5
chr7 0.75
chr9 1
chr9 1
chr22 0.5
chr22 0.5
where the first column is the chromosome location and the second column is
some value. What I'd like to do is have a histogram created for each chr
location (i.e. a separate histogram for chr1, chr2, chr3, chr7, chr9, and
chr22). I am just
2008 Feb 10
11
data frame question
Hello
I have 2 data frames df1 and df2. I would like to create a
new data frame new_df which will contain only the common rows based on the first 2
columns (chrN and start). The column score in the new data frame
should
be replaced with a column containing the average score (average_score) from df1
and df2.
df1= data.frame(chrN= c(“chr1”, “chr1”, “chr1”, “chr1”, “chr2”,
“chr2”, “chr2”),
2011 Jun 08
1
return counts of elements on a table column depending on elements on another column
Hi,
I am given the following table:
> head(hsa_refseq)
chr genome region start stop nu strand nu.1 nu.2
gene_id
1 chr1 hg19_refGene CDS 67000042 67000051 0 + 0 gene_id
NM_032291
2 chr1 hg19_refGene exon 66999825 67000051 0 + . gene_id
NM_032291
3 chr1 hg19_refGene CDS 67091530 67091593 0 + 2 gene_id
NM_032291
4 chr1 hg19_refGene exon
2011 Oct 19
1
replacing percentage of values in data frame
I've been looking for how to change a certain percentage of values in a data
frame, but I've been struggling to find information in R.
For example:
#################example data##############
> data
V1 V2 V3 V4 V5 V6 V7
1 chr1 500 500 CHH 0 0.5 +
2 chr1 550 550 CHH 0 0.0 +
3 chr2 700 700 CHH 0 0.0 +
4 chr2 1000 1000 CHH 0 0.0 +
5 chr3
2010 Nov 07
1
How do I order xyplot line points?
I have the following xyplot figure:
http://img577.imageshack.us/img577/686/filesizeresults12000000.png
The data are organized in a matrix file as follows:
Type Elements Chromosome Time
bedGz 12000000 chr1 14.240
bedGz 12000000 chr2 7.949
bedGz 12000000 chr3 5.103
bedGz 12000000 chr4 5.290
bedGz 12000000 chr5 5.161
...
The x-axis labels in the Chromosome column are ordered
2008 Feb 18
3
remove column names from a data frame
I want to remove the column names from a data frame. I do
it the long way, can any body show me a better way ?
df= data.frame(chrN= c(“chr1”, “chr2”, “chr3”), start= c(1,
2, 3), end= c(4, 5, 6), score= c(7, 8, 9))
df
#I write a txt file without row or column names
write.table(df,"df1.txt",sep='\t',quote=FALSE,row.names=F,col.names=F)
#then I read it with the header = F
2012 Jul 02
1
apply with multiple conditions
Hello all,
I have written a for loop to act on a dataframe with close to 3million rows
and 6 columns and I would like to pass it to apply() to speed the process up
(I let the loop run for 2 days before stopping it and it had only gone
through 200,000 rows) but I am really struggling to find a way to pass the
arguments. Below are the loop and the head of the dataframe I am working on.
Any hints
2010 Feb 18
2
3D plot
Dearl list,
can anyone point me to a function or library that can create a graph similar to the one in the following powerpoint presentation?
http://bmi.osu.edu/~khuang/IBGP705/BMI705-Lecture7.ppt
(pages 36-37)
In order to try to explain the graph, the way I see it in R terms is something like this:
the "p-q" axis is a vector of positions (for example, seq(0,5000000,1))
the
2008 Dec 24
1
Conditional Counting with Table
Dear all,
I have the following data frame:
V1 V2
aaa chr1
aaa chr2
aaa NM
aaa QC
aaa chr10
att NM
att chr7
What I want to do is to count the string (V1).
But the condition of counting is: if the V2 of the string
is "NM" or "QC" then the count is not increased.
Hence the contigency table will look like this:
#tag count
aaa 3
att 1
Is
2010 Oct 01
1
[Help]:How to use "loop" to achieve this aim?
Hello, Everyone,
how to use "loop" to make the process automatic and fast?
When compute each sample, the script type in R almost the same, just the
input and output file's name is changed(chr1 change to chr2, chr3,chr4...).
The first sample's script like this:
>chr1=MEDIPS.readAlignedSeqences(BSgenome="hg19", file="chr1",numrows= )
2011 Oct 25
4
comparing two tables
Hi everybody,
I would like to know whether it is possible to compare to tables for certain
parameters.
I have these two tables:
gene table
name chr start end str accession Length
gen1 4 646752 646838 + MI0005806 86
gen12 2L 243035 243141 - MI0005821 106
gen3 2L 159838 159928 + MI0005813 90
gen7 2L
2012 Mar 02
3
subseting a data frame
HI,
this is my problem I want to subset this file df, using only unique
df$exon printing the line once even if df$exon appear several times:
unique(df$exon) will show me the unique exons
If I try to print only the unique exon lines
with df[unique(df$exon),] -this doesn't print only the unique ones :(
could you help?
thanks
Nat
exon size chr start