similar to: FW: Index out SNP position

Dear R experts, I have 2 matix: A& B. I am trying to index B against A - (1) find out B rows that fall between the col 1 and 2 of A& put them into a new vector SNP.I made code as below, but I cannot think of a right way to do it. Could anyone help me with the code? Thanks,Jiang---- A <-

Hi everyone, I have a data frame Gene with SNPs eg. P1 P2 P3 CG CG GG -- -- AC -- AC CC AC -- AC I tried to replace all the GG with a value 3. Gene[Gene=="GG"]<-3 It always give me: Warning in `[<-.factor`(`*tmp*`, thisvar, value = 3) : invalid factor level, NAs generated Does any know if there is anything wrong with my code? Thanks, Zhengyu

Dear R experts, I have two matrix (seq & mat) & I want to retrieve in a new matrix all the numbers from mat that =1 (corresponding to the same row/ column position) in seq, or all the numbers in mat that =-1 in seq. - Replace all the numbers with NA if it's not 1/-1 in seq. There are some "NA"s in seq. seq=matrix(c(1,-1,0,1,1,-1,0,0,-1,1,1,NA),3,4)

No html!, Copy the list using Reply-All. The data frame group_PrivateLabel does not contain variables called Product_Name or Region. David C From: nguy2952 University of Minnesota <nguy2952 at umn.edu> Sent: Friday, June 1, 2018 2:13 PM To: David L Carlson <dcarlson at tamu.edu> Subject: Re: [R] Regroup and create new dataframe Hi David, your example is perfect! I am still

Responses should be copied to r-help using ReplyAll. You are still sending html formatted emails. If you are using Microsoft Outlook, click the Format Text tab and select ?Aa Plain Text?. No one has asked you to reveal the data set, only to create one with a similar structure. Is the data I sent reasonably close? What should it look like after it is transformed? David C From: nguy2952

Thanks again. I am going to try the different versions. But I probably won't be able to get to it till next week. This is probably at the point where anything further should be sent to me privately. -Roy > On Jun 1, 2017, at 1:56 PM, David L Carlson <dcarlson at tamu.edu> wrote: > > On the off chance that anyone is still interested, here is the corrected function using

I'm not sure how you are incorporating time period into your data structure. Typically we are looking at plots or assemblages as the rows and taxa as the columns. Time period adds a third dimension that could be added as blocks of rows. For example, depending on the resolution of your data, one approach would be to have up to 8 rows for each locality: Loc1.1000, Loc1.2000, . . . Loc1.8000. If

On the off chance that anyone is still interested, here is the corrected function using aperm(): z <- array(1:120,dim=2:5) f2 <- function(a, wh) { idx <- seq_len(length(dim(a))) dims <- setdiff(idx, wh) idx <- append(idx[-1], idx[1], wh-1) aperm(apply(a, dims, rev), idx) } all.equal(f(z, 1), f2(z, 1)) # [1] TRUE all.equal(f(z, 2), f2(z, 2)) # [1] TRUE

We need to keep the discussion on the list. When I run your code, there are several problems. strain.data <- read.xlsx("Dee rhiz.xlsx", sheetName ="strain", header = T, row.names = 1) str(strain.data) # lists 9 columns at the end with all NAs strain.data1 <- (strain.data, sqrt.dist = TRUE) # this is not a valid R line. I get Error: unexpected ',' in

Thanks to all for responses/. There was a question of exactly what was wanted. It is the generalization of the obvious example I gave, >>> junk1 <- junk[, rev(seq_len(10), ] so that junk[1,1,1 ] = junk1[1,10,1] junk[1,2,1] = junk1[1,9,1] etc. The genesis of this is the program is downloading data from a variety of sources on (time, altitude, lat, lon) coordinates, but all

Hi, I want to make a plot similar to sm1 (attached). The code I tried is: dcols <- densCols(x,y) smoothScatter(x,y, col = dcols, pch=20,xlab="A",ylab="B") abline(h=0, col="red") But it turned out to be s1 (attached) with big dots. I was wondering if anything wrong with my code. Thanks,Zhengyu -------------- next part -------------- A non-text

Hello Dave Here is the code I have tried. getwd() setwd("D:/BAP Session/Nuance") getwd() AmbientTr <- read.csv("AmbientBatchbox.csv", stringsAsFactors = TRUE) str(AmbientTr) summary(AmbientTr) install.packages("ggplot2") library(ggplot2) boxplot(RTF~Batch,data=AmbientTr, ylim = c(0,30), main="RTF By Batch", xlab="Batch",

> On 24 Oct 2017, at 22:45 , David L Carlson <dcarlson at tamu.edu> wrote: > > You left out all the most important bits of information. What is yo? Are you trying to assign a data frame to a single column in another data frame? Printing head(samples) tells us nothing about what data types you have, especially if the things that look like text are really factors that were created

Hi Peter, Thanks for contributing such a great answer. Can you please provide a pointer to the documentation where it explains why dd$B <- s and dd["B"] <- s have such different behavior? (I am perfectly happy if you write the explanation but if it saves you time to point to some reference that works fine for me.) Regards, Eric On Wed, Oct 25, 2017 at 2:27 PM, Peter Dalgaard

Dear All, This problem is over. Clock24.plot did the job. Thanks to all those who assisted me. Ogbos On Apr 22, 2016 8:34 PM, "Ogbos Okike" <giftedlife2014 at gmail.com> wrote: > Dear All, > One hand. Many thanks!! The code run as soon as I loaded lubridate. > > Please can you guide me on how to relate this code to my actual data. > My actual data is looking like:

No. You have not used it correctly. It was an example. Put your commands between the two sink functions. That will save any printed out put that results from those commands. It will not save attr, but you did not ask how to do that. David C On Nov 1, 2017 12:21 PM, Priya Arasu <galaxie2485 at yahoo.co.in> wrote: Hi David, Thank you for the example. When I try to use the cat function, I get

Hi, Does anybody know how to obtain the imputed SNP genotype probabilities from the snpStats package? I am interested in using an imputation method implemented in R to be further used in a simulation study context. I have found the snpStats package that seems to contain suitable functions to do so. As far as I could find out from the package vignette examples and its help, it gives the

Hi, In addition to GADA, what are the available package in R and bioconductor to analyze amplification, deletion, LOH and indels of CNV, SNP data? Any reference is welcome. Best, Carol

I'm having trouble getting summaries out of the 250K snp chips in R. I'm using the oligo package and when I attempt to create the necessary SnpQSet object (to get genotype calls and intensities) using snprma, I encounter memory issues. Anyone have an alternative package or workaround for these large snp chips? -- View this message in context:

Hello, I would like to plot specific SNPs with their exact locations on a chromosome. Based on my genotyping results I would like to separate these SNPs in three different categories: 1, 2 and 3 and use different colours to represent these categories. The script below generates the sample data. I can plot these with the image function using the following: val <- 1:3 samp <- sample(val,