Displaying 20 results from an estimated 600 matches similar to: "'Record' row values every time the binary value in a collumn changes"
2016 Mar 04
2
llvm-cov accepting many binary files for aggregated coverage reports
Hi All,
I want to provide a solution that presents code coverage reports that
include the aggregated code-counts across many binaries. Our test
engineers currently do this using gcov-mode by merged .gcda data files. We
can do a similar merge of the .profraw files, so that the many binaries are
represented in one .profdata file; However, llvm-cov will only generate
reports based on one binary at
2009 Sep 27
2
Count number of zeros in a collumn
I have a matrix 700x2000 which is sampled in each cycle from another matrix
788x2000 with the numbers 0,1 and 9
There is one specific collumn of this matrix, dart[,1977], that usually,
after the samplimg procedure has only 1 and 9 (because the zero frequency in
this collumn is low).
However, when this happens, I want to include an IF conditional in my code.
so basically what i wanted to do was to
2010 Aug 04
4
Adding collumn to existing data frame
Hi experts,
I am trying to write a very flexible method that allows me to add a
new column to an existing data frame. This is what I have so far:
add.column <- function(df, new.col, name) {
n.row <- dim(df)[1]
length(new.col) <- n.row
names(new.col) <- name
return(cbind(df, new.col))
}
df <- NULL
df <- data.frame(a=c(1,2,3))
df
# corect: added NA to new collumn
df <-
2009 Nov 05
4
collumn error when exporting to Excel
Dear all,
I am attempting to export my results (data.frame) created with the help of a number of you to Excel.
In the procedure my column structure is however lost and all results are placed together into the first Excel column.
I have tried: write(), write.table(), write.matrix(), export() and have the same results. I Have checked the import/export FAQ and did a Google search to no avail.
Any
2009 Nov 20
1
how to specify the order of panels with xyplot
> chromosomes
id refseq name length
1 0 NC_000001.9 Homo sapiens chromosome 1 247249719
2 1 NC_000002.10 Homo sapiens chromosome 2 242951149
3 2 NC_000003.10 Homo sapiens chromosome 3 199501827
4 3 NC_000004.10 Homo sapiens chromosome 4 191273063
5 4 NC_000005.8 Homo sapiens chromosome 5 180857866
6 5 NC_000006.10 Homo sapiens chromosome 6
2004 Aug 06
1
questions related to ploting in R
Dear all.
I need to draw a scatter plot of 23 chromosome copy numbers (y axes) against
chromosome and physical location within each chromosome in one plot. The
data matrix looks as below:
chr location copy_num
1 118345 1.320118
1 3776202 1.133879
1 4798845 0.989997
1 5350951 1.100967
. more data here
.
.
2 118345 2.459119
2 157739 1.915919
2 1530065 1.924372
2
2010 Jun 01
5
Help barplots
Dear All,
I am newbie to R, and I wanted to plot a barplots with R and in such a way
that It will also show me position which I can plot on the bar line.
Here is my code that I am using to plot,
> chromosome <- c(40.2, 35.6, 36.1, 29.6, 31, 29.6, 31, 29.4, 28.2, 23, 23,
28.2)
>barplot (chromosome, col="purple", xlab="Oryza sativa Chromosomes", border
= NA, space =
2012 Sep 10
3
plot: x and y chromosomes are missing
Hello,
I have a list with gene names, fold changes (=expression level) and
chromosomes.
Names fold change chromosome
hz 1.5 2
If I plot fold change versus chromosome (or vice versa):
plot (ch, fc)
I see only the chromosomes with numbers but not those with letter (x and
y). What can I do?
A second question:
How can I add a single line in that plot at a certain
2009 Dec 04
1
Lattice : Help with changing the labels of x-axis in respective panels
Dear R-Helpers,
I am not very experienced in using lattice and I am still in the learning
stage
I have a data set which looks like this: (I have deleted a few lines in
order to save space)
Chromosome marker Marker.Name Distance
1 1 1 PeMm261 0.0000
2 1 2 Xtxp8 10.1013
..
20 1 20 EbMi148 210.3099
21 1 21 Xtxp25
2007 Apr 02
3
Random number from density()
Hello,
I'm writing some genetic simulations in R where I would like to place
genes along a chromosome proportional to the density of markers in a
given region. For example, a chromosome can be presented as a list of
marker locations:
Chr1<-c(0, 6.5, 17.5, 26.2, 30.5, 36.4, 44.8, 45.7, 47.8, 48.7, 49.2,
50.9, 52.9, 54.5, 56.5, 58.9, 61.2, 64.1)
Where the numbers refer to the locations of
2008 Jul 09
2
replacing value in column of data frame
Dear all,
Probably a very basic question but I need some help.
I have a data frame (made by read.table from a text file) of microarray data, of which the first column is a factor and the rest of the columns are numeric.
The factor column contains chromosome names, so values 1 through 22 plus X, Y and XY. The numeric columns contain positions or intensity measurements.
What I need to do is
2012 Jul 13
2
alternate tick labels and tick marks with lattice xyplot
Hi,
I would like to use xyplot to create a figure. Unfortunately, I cannot find
documentation in xyplot to specify alternating the x-axis tick labels with
the x-axis tick marks. I can do this with the regular R plot function as
follows.
#A small version of my data looks like this
data<-data.frame(matrix(ncol=3,nrow=12))
data[,1]<-rep(c(1,2,3),c(4,4,4))
data[,2]<-rep(c(1,2,3,4),3)
2010 Feb 10
2
How to create probeAnno object?
Hi,
I want to use segChrom() method in tilingArray package. For that I need to create a probeAnno object. I could not find much much info by ?probeAnno. I need help in creating probeAnno object.
Snap shot of the file(.txt):
chr1 2500014 2500038 + 0.232689943122845
chr1 2500039 2500063 + 2.60502410304227
chr1 2500062 2500086 + 0.0756595313279895
chr1 2500080 2500104 + 0.78574617788405
chr1
2008 Jul 08
2
list genes w/n a genomic fragment
Hi, is there any package/function in Bioconductor that can do this: if given
the chromosome positions of a fragment, find out all genes within, and with
the information about which strand is the sense strand. And vice versa.
Thanks a lot.
-----
Appreciate your time & attention!
--
View this message in context: http://www.nabble.com/list-genes-w-n-a-genomic-fragment-tp18331452p18331452.html
2007 Mar 01
1
object is not subsettable
Dear colleagues,
I've just come across a problem with the following command which is a
part of the "metaOverview.R" code file provided as an monography-
accompanying file at
http://www.bioconductor.org/docs/mogr/metadata:
##################################
R> hasChr <- eapply(GOTERM, function(x)
+ x[grep("chromosome", Term(x))])
Error in
2009 Jan 15
3
How to create a chromosome location map by locus ID
Hi,
I'm trying to make a chromosomal map in R by using the locus. I have a list
of genes and their locus, and I want to visualise that so you can see if
there are multiple genes on a specific place on a chromosome. A example of
what I more or less want is below:
http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG
The genes and locus are here:
2011 Oct 04
1
Assigning genes to CBS segmented output:
Hi All,
I have an CBS segmentation algorithm output for 10 tumor samples each from 2
different tumors.
Now, I am in an urgent need to assign gene (followed by all genes present)
that belong to a particular segment after I removed all the CNVs from
segment data. The format of the data is:
Sample Chromosome Start End Num_Probes Segment_Mean
Sample1A-TA 1 51598 76187 15
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
2011 Dec 09
1
minor allele frequency comparison
Hi all,
We are using two methods to identify SNPs. One is based on resequencing
the genome and aligning the reads to the sequenced genome to identify SNPs
(data available for 44 individuals). Another is based on SNP array with
selected loci (30000 loci, 870 individuals). I want to compare the results
from the resequencing based minor allele frequency and Array based minor
allele frequency.
2003 Jan 16
1
graphics
Dear R community,
I need to plot the results of some simulations I did using QTL
Cartographer. I am plotting LOD scores over three chromosomes. The three
plot have to be one next to the other.
The procedure I am using is:
par(mfrow=c(1,3))
plot(x$x, x$y, ylim=c(0,35), type="l", col="blue", las=1, xaxs="i",
yaxs="i", xlab="X Chromosome",