search for: lalithaviswanath

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 .... .... ....

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

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

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

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

Hi I have data of the following form ID age member_FLAG 1 25 Y 2 36.75 N 3 75.5 N ......... ......... I want to get a histogram of this data showing distribution of member_flag in each age-bin i.e. how many values in each age bin have a member_flag of 'Y' and how many have 'N'. I was able to do the same using barplot2. However I also need similar

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

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

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

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 =

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 =

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

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 =

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