Re: [R] How to extract data based on first column ID in R

Thanks, David, It is resolved now. I used below code dim(otu.list) [1] 196 1 i <- row.names(data) %in% otu.list[[1]] Thanks Yogesh On Sun, 23 Jun 2019, 21:38 David Winsemius, wrote: > > > On Jun 23, 2019, at 5:57 AM, Yogesh Gupta wrote: > > > > Hi, > &

Re: [R] How to allow duplicate names in R

tes in your data, and consider options such as removing > duplicates, re-labelling duplicates, or aggregating the values > corresponding to duplicates (e.g. mean, median, max...) before plotting so > that the result will be meaningful to the viewer. > > On June 23, 2019 10:54:34 AM P

Re: [R] How to allow duplicate names in R

A") Thanks Yogesh On Sun, Jun 23, 2019 at 6:32 PM Yogesh Gupta wrote: > Hi, > > I do have duplicates names in tab delimited files, I need to allow to read > these duplicate names in R, > > Could you please suggest how can modify this code to allow to read > dup

[R] How to allow duplicate names in R

Hi, I do have duplicates names in tab delimited files, I need to allow to read these duplicate names in R, Could you please suggest how can modify this code to allow to read duplicates names: x<-read.table("HEATMAP.ROOT.input.txt",sep="\t",head=T, check.names=FALSE) > x Gen

Re: [R] How to filter data in R based on first column ID

e both are tab delimited text files. *Thanks* *Yogesh* On Sun, Jun 23, 2019 at 4:22 PM Yogesh Gupta wrote: > Hi Rui, > > Thanks for your help. but still I did not able to get the data. > > > dput(head(data)) > > structure(list(`Root-1.S35.L001` = c(0, 0, 0, 0, 0, 0.0467

Re: [R] How to filter data in R based on first column ID

Root.33.S27 Root.35.S37 [41] Root.36.S47 Root.37.S57 Root.38.S67 Root.42.S77 [45] Root.44.S7 Root.46.S18 Root.48.S28 Root.49.S38 [49] Root.5.S45 Root.52.S48 Root.53.S58 Root.6.S55 [53] Root.7.S65 Root.8.S75 <0 rows> (or 0-leng

Re: [R] How to filter data in R based on first column ID

a vector and in R it's not > expected to have a dim attribute. What would have made sense would have > been > > length(i) > sum(i) > > > Hope this helps, > > Rui Barradas > > > Às 11:41 de 23/06/19, Yogesh Gupta escreveu: > > Hi R

[R] How to extract data based on first column ID in R

Hi, I need help to extract data based on first column ID in R. I used the below code but not succeed , it is not giving the row values, only showing the header of rows. > head(data) Root-1.S35.L001.Root-10.S75.L001 71f84e7910006f22684121564206e8ca 0.0 03b167

[R] How to filter data in R based on first column ID

) 719e20e1e3d19fbc5dd50844c6d29a8f bfffa74c0971b30ccf3b19f65911801f 62a5c6f5e0adda662739a7ac521ea790 I will be tankful for your help. Thanks Yogesh *Yogesh Gupta* *Research Fellow* *Institute for Global Food Security* *Queen's University* *Belfast, UK* [[alternative HTML version de

[R] How to plot dendogram based on samples ID

Hi, I do have RNAseq FPKM count and interested in dendrogram for samples cluster. I used below code but it generate dendogram based on ContigID instead of sampleID. > countMatrix = > read.table("Trinity_trans.counts.matrix.txt",header=T,sep='\t',check.names=F,row.names=1) > dim(countMatrix) [1

[R] Getting error in dendogram based on gene expression

ust(d, method = "complete") Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: Thanks Yogesh -- *Yogesh Gupta* *Postdoctoral Researcher* *Department of Biological Science*

[R] getting error while trying to make dendogram based on gene expression

I am trying to make dendogram based on gene expression matrix , but getting some error: I countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F) colnames(countMatrix) count_matrix <- countMatrix[,-1] # remove first column (gene names) rownames(count_matrix)

[R] error while creating a simple graph

Dear All, I am learning R so it's a very simple problem but I do not understand while I am not able to generate a graph from two vectors. when I type this code, it generates a very nice graph. pdf("mygraph.pdf") > attach(mtcars) > plot(wt,mpg) > abline(lm(mpg~wt)) > title("Regreesion of mpg") >

[R] Dendogram from RNAseq read count to show correlation between biological replicate using R

Dear all, I need to make dendogram from read count in a csv file across 34 samples including biological replicate. Please share R code or package to do this. Do I also need to normalized read count before using read data? Thanks [[alternative HTML version deleted]] ___

[R] DESeq2 pairwise compasion

construct a DESeqDataSet: dds <- DESeqDataSetFromMatrix(countData = countMatrix, colData = colData, design = ~ condition) Thanks Yogesh -- *Yogesh Gupta* *Postdoctoral Researcher* *Department of Biological Science* *Seoul National University* *Seoul, South Korea* [

[R] error while opening vignette DESeq2

R/library/DESeq2/doc/DESeq2.pdf' -- *Yogesh Gupta* *Postdoctoral Researcher* *Department of Biological Science* *Seoul National University* *Seoul, South Korea* [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -

[R] Problem related to rowSums

Hi... I have a dataframe with n columns and n rows. I need to find how many rows contains zero raw read count across all column. Thanks -- *Yogesh Gupta* *Postdoctoral Researcher* *Department of Biological Science* *Seoul National University* *Seoul, South Korea* [[alternative HTML

[R] Getting error in clustering analysis of RNAseq raw reads

;) *** caught segfault *** address 0x7f51c12c0228, cause 'memory not mapped' Traceback: 1: hclust(d, method = "ward.D2") Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving wo

[R] Error in DESeq Installation

= lib, ...) : installation of package ‘geneplotter’ had non-zero exit status 6: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘DESeq’ had non-zero exit status Thanks *Yogesh Gupta* *Postdoctoral Researcher* *Department of Biological Science* *Seoul National University

[R] Error In DESeq installation

nductor version 3.4 cannot be upgraded with R version 3.3.1 Can you suggest me I How I can resolve it. Thanks Yogesh *Yogesh Gupta* *Postdoctoral Researcher* *Department of Biological Science* *Seoul National University* *Seoul, South Korea* web) http://biosci.snu.ac.kr/jiyounglee