Displaying 20 results from an estimated 3000 matches similar to: "Query about using table"
2006 May 01
4
table of means/medians across bins used for a histogram
Hi
I am trying to get a table of means of parameter 1
across BINS of parameter 2.
I am working in proteomics and a sample of my data is
as follows
cluster-age clock-rate(evolutionary rate) scopclass
0.002 10 A
0.045 0.1 B
0.13 15 A
0.15 34 D
....
....
....
2007 Jan 23
3
Query about extracting subsets from a table
Hi
I am trying to process tabular data as follows:
Data in the input file is of the form
genome1 genome2 tree-dist log10escore
Genome1 and genome2 are alphabetic.
Tree-dist and log10escore are numeric.
I wish to extract only those rows from this table
where the log10escore is less than -3.
data <-read.table(filename);
data$log10escore = data$log10escore[ data$log10escore
< -3];
I
2007 Feb 28
3
Packages in R for least median squares regression and computing outliers (thompson tau technique etc.)
Hi
I am looking for suitable packages in R that do
regression analyses using least median squares method
(or better). Additionally, I am also looking for
packages that implement algorithms/methods for
detecting outliers that can be discarded before doing
the regression analyses.
Although some websites refer to "lms" method under
package "lps" in R, I am unable to find such a
2006 Jul 11
1
Query about getting averages across a certain parameter in a table
Hi
I have a table that goes
data
cluster_ac clockrate age class
7337 0.9 0.001 alpha_proteins
7888 0.1 0.78 beta proteins
etc
The class column can have 7-8 different unique values
While the clockrate and age columns are floats varying
from 0 to 1.
I wish to get the average clockrate across each of the
classes for this data.
I would appreciate your help
2007 Mar 01
2
Query about data manipulation
Hi
Thanks much for the prompt response to my earlier
enquiry on packages for regression analyses.
Along the same topic(?), I have another question about
which I could use some input.
I am retreiving data from a MySQL database using
RODBC.
The table has many BLOB columns and each BLOB column
has data in the format
"id1 \t id2 \t measure \n id3 \t id4 \t measure...."
(i.e. multiple rows
2007 Jan 26
1
Package for phylogenetic tree analyses
Hi
I am looking for a package that
1. reads in a phylogenetic tree in NEXUS format
2. given two members/nodes on the tree, can return the
distance between the two using the tree.
I came across the following packages on CRAN
ouch, ape, apTreeShape, phylgr all of which seem to
provide extensive range of functions for reading in a
Nexus-format tree and performing phylogenetic
analyses, tree
2007 Jan 25
1
unique/subset problem
Hi
I am new to R programming and am using subset to
extract part of a data as follows
names(dataset) =
c("genome1","genome2","dist","score");
prunedrelatives <- subset(dataset, score < -5);
However when I use unique to find the number of unique
genomes now present in prunedrelatives I get results
identical to calling unique(dataset$genome1) although
2007 Jan 22
2
Query about using optimizers in R without causing program to crash
Hi
I am a newbie to R and am using the lm function to
fit my data.
This optimization is to be performed for around 45000
files not all of which lend themselves to
optimization. Some of these will and do crash.
However, How do I ensure that the program simply goes
to the next file in line without exiting the code with
the error
"Error in lm.fit(x, y, offset = offset, singular.ok =
2007 May 02
3
Query about finding correlations
Hi
I have a dataframe which has 3 columns of numeric data
A,B,C each of which has been obtained independent of
the other.
We are trying to find out, which of A or B cause C
i.e. We are hypothesising that C is the effect and
either A or B, not both is the cause.
i.e. A causes C and this cause-effect relationship
explains B.
The data for A contains more noise than that for B.
We are working with
2007 Mar 12
2
Query about substituting characters in a df
Hi
I have a data frame with 40,000 rows and 4 columns,
one of which is "class".
For each row, the "class" column can be one of 10
possible NUMERIC values.
I wish to substitute these numeric values with
words/characters.
For example, I wish to substitute all occurences of
"5467" in the column "class" with "alpha", "7867" with
2007 Jan 24
1
Query about extracting subset of datafram
Hi
I have a table read from a mysql database which is of
the kind
clusterid clockrate
I obtained this table in R as
clockrates_table <-sqlQuery(channel,"select....");
I have a function within which I wish to extract the
clusterid for a given cluster.
Although I know that there is just one row per
clusterid in the data frame, I am using subset to
extract the clockrate.
clockrate =
2007 May 02
1
Query about RODBC to access MySQL from Windows
Hi
I am trying to use RODBC in R installed on Windows to
access MySQL database (on a linux box).
I set up a DSN and specified this DSN in R as follows
library(RODBC);
channel <- odbcConnect("mysqldsn");
RODB Connection 5
Details:
case=nochange
PORT=3306
........
Although this seems to connect properly, running any
command yields NO results.
i.e. sqlQuery(channel, "show
2007 Jan 22
1
Query about using try block
Hi
Thanks for your response.
However I seem to be doing something wrong regarding
the try block resulting in yet another error described
below.
I have a function that takes in a file name and
does the fit for the data in that file.
Hence based on your input, I tried
try ( (fit = lm(y~x, data = data_fitting)), silent =
T);
I left the subsequent lines of my code unchanged.
coeffs =
2009 Mar 22
1
barplot2 x-axis
Dear R users,
I am trying to build a barplot2 graph however I can't find a way of defining
the scale for the x-axis.
I would like to show in my x-axis only the numbers 0, 25, 50, 75 etc. (so
far R is giving me a random scale hard to interpret and it doens't look
nice...). Could anyone advise me on how to do this please, it would be a
great help! Thank you.
Below I show the code I have
2017 Jan 27
4
Suggestion: barplot function
Hello developers folks!
First, congratulations for the wonderful work with R.
For science, barplots with error bars are very important. We were
wondering that is so easy to use the boxplot function:
boxplot(Spores~treatment, col=treatment_colors)
But there is no such function for barplots with standard deviation or
standard error. It becomes a "journey" to plot a simple graph (e.g.
2009 Sep 15
2
Viewing Function Code
Hi All,
I'd like to see the function code behind the barplots2() function in the
gplots package, however i come across a bit of a stumbling block of a hidden
function, can anyone help?
> library(gplots)
> methods(barplot2)
[1] barplot2.default*
Non-visible functions are asterisked
> barplot2
function (height, ...)
UseMethod("barplot2")
<environment:
2003 Aug 07
1
abline() plot order
I am performing this sequence
barplot
title
legend
abline
When abline renders the lines they appare to be in the layer
above the bars in the graph. Is there a way to make them
render first or 'behind' the bars?
Thanks.
2004 Nov 26
2
barplot(2?) with CI from a zero reference line
Dear R Users, (and dear Marc)
First of all many thanks for the answers to my previous questions.
I would like to barplot the mean percent change of a variate with it's
CI. Bars should start from the zero reference line to height (in
barplot2).
Is there a way to tweak barplot2, for example, to do that ?
I have tried to see what the function was but unlike other functions was
not able to
2004 Nov 24
1
reshaping of data for barplot2
Dear All,
I have the following data coming out from
s <- with(final,
summarize(norm, llist(gtt,fdiab),
function(norm) {
n <- sum(!is.na(norm))
s <- sum(norm, na.rm=T)
binconf(s, n)
}, type='matrix')
)
ie
gtt fdiab norm.norm norm.norm2 norm.norm3
18
2007 Oct 31
2
ylim in barplot2 function?
Hi list,
I'm using barplot2 form the gplots package to plot a few numbers (I want to add SD bars later).
However, I would like the y-axis not to start from 0 but 500. When I add the parameters YLIM, something goes wrong. The graph is not 'cut off' at 500. Instead the bars seems to sink trough the bottom of the graph.
Because its a little hard to explain, here is a self-containing