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Questions tagged [r]

Please supplement your question with a minimal reproducible example. Use dput() for data and specify all non-base packages with library calls. For statistical questions please use http://stats.stackexchange.com.

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1answer
5 views

Matching these matrices in R

I have two matrices; I want to convert the row names of first matrix to gene symbol from matched ensemble=gene symbol from second matrix ...
2
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1answer
60 views

Differentially methylated position analysis in a related sample?

I'm trying to figure out how to do a DMP analysis (using minfi dmpFinder) on a related sample (if it's even possible). Right now the code (not written by me) is: ...
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0answers
28 views

Geneland R + Fortran error?

I am helping an undergrad with their project and their thesis advisor has requested they use GENELAND for their analysis. I haven't worked on this sort of analysis, so all I have done is install it in ...
3
votes
1answer
34 views

How can I assign a genomic region into a window using R?

I have asked this question at BioStars but have not gotten any suggestions so far. So, I am asking the community here, perhaps someone here has an idea how I can solve my problem. I am dealing with a ...
0
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1answer
29 views

Error in formation of correlation matrix-(corrupt matrix — dims not not match length)

I am working on a script to create a correlation matrix and mutual_rank matrix from RNAseq gene counts for 57992 genes in 7027 samples. I have already tested this script for a smaller file (for 10,000 ...
1
vote
1answer
11 views

cn.MOPS fails with 'missing value where TRUE/FALSE needed'

I am trying to use cn.MOPS to call CNVs on a set of whole exome sequencing data bam files. My script (up to the point where it fails) is: ...
0
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1answer
32 views

Where can I find .cdf files for Affymetrix ChIP-chip data analysis?

I am analysing microarray ChIP data generated several years ago. I want to use the affy package for R. However, in order to load the CEL files and proceed with the analysis, I need the pombe ...
3
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0answers
57 views

Getting genes specially up or down regulated

I have 6 RNA-seq samples like this 4 patients (005, 036, 121, 013) I have 3 tumour samples and 3 cancer models (organoid) This is PCA of log transformed data by ...
1
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1answer
42 views

Understanding PCHeatmap outputs

I am currently trying to understand the purpose of these PCHeatmaps - part of the seurat package in R: All the online documentation I have searched for has only ...
1
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1answer
41 views

GBS: clustering of PCoA axes with R package mclust to describe identity by missingness

I have a SNP dataset with 56 populations and 430 samples that was produced by GBS sequencing. I need to identify groups of samples that have similar patterns of genotype missingness, since there is ...
2
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1answer
33 views

scRNASeq expression matrix with decimal values

I am trying to replicate some results of a scRNASeq experiment and, when I looked at the data provided by the author, I noticed that some of the counts in the expression matrix are represented as ...
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0answers
38 views

Mutation annotation to the heatmap

I have mutation data of patients.How do i add that mutation info or annotate those as column with my annotation information expression and mutation To help myself i did try this Zuguang Gu but couldn;...
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2answers
55 views

Error in adding data in columns of R data frame

This is my file ...
0
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1answer
35 views

Combat for multiplatform batch correction

I have been looking ways to use data from various micro-array platform such as agilient, rosetta/merk. Some of the established method I came across is combat, but I'm not sure if it can be done for ...
0
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1answer
39 views

Finding the members in a confusion matrix

I have inferred a confusion matrix of training and test set by neural network. I want to know which members are in the confusion matrix. ...
1
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0answers
21 views

failed to install hdf5r [duplicate]

I failed to install hdf5r using this command provided by https://satijalab.org/seurat/mca_loom.html: devtools::install_github(repo = 'hhoeflin/hdf5r'),below is the code,can you help me ?
0
votes
1answer
86 views

R studio failed to install the latest development version of hdf5r from Github (win10)

I install hdf5r following https://github.com/hhoeflin/hdf5r, it shows two methods: When I use the second method to install from github,it showed many errors: ...
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2answers
63 views

How can I obtain the percentage gene expression per identity class in Seurat as further processible numbers (e.g. matrix)?

I am analysing my single cell RNA seq data with the Seurat package. I want to know if there is a possibilty to obtain the percentage expression of a list of genes per identity class, as actual numbers ...
2
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3answers
120 views

Question about Co-expression analysis and finding targets for lncRNAs

I have a dataset with 88 tumor and 113 normal samples. Among the 50k genes after filtering there are a total of 28k genes (both mRNAs and lncRNAs) I wanted to do co-expression analysis between ...
0
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1answer
54 views

Extracting modules from corelation and then module clustering

This is the paper where they have first done co-expression analysis of TF and then found coexpressed modules which were further subjected to module clustering ,paper So now im clear about the first ...
1
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1answer
63 views

Percentage distribution of cells in all clusters based on their treatment condition?

I have 2151 cells, I clustered them by Seurat to 5 clusters. With the code below, I am able to have the number of cells per cluster and per condition: ...
2
votes
1answer
45 views

How to model the effect of acid/base on pH

I would like to model a biological compartment with sysBio R package. It is fine but I'm having a difficult time with modeling the change in pH due to acidosis. I tried several things like: ...
4
votes
1answer
39 views

Gene Ranking - signal to noise ratio used in GSEA-P algorithm?

I'm looking at Broad Institute's orignal GSEA-P algorithm R script which I downloaded here: http://software.broadinstitute.org/gsea/downloads.jsp. I'm trying to adapt their GSEA.1.0.R script to ...
2
votes
1answer
58 views

How I know which gene is a good predictor in this neural network or not?

I have 25 highly differentially expressed genes among responder (TRG12) and non responder (TRG45) patients to chemotherapy. I have made a neural network of these genes. Accuracy of model is 0.73 but ...
2
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1answer
24 views

Pathway plot in GeneTrail data base

So I'm doing a pathway analysis using GeneTrail database. One thing I am not able to get is this similarity measure being calculated and plotted: I want to know how this is being made, what is the ...
1
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0answers
37 views

Output the linear predictor from a stratified cox model?

I have fitted a cox model on a pooled dataset of multiple studies, say study A, B and C. As these studies have different baseline hazard functions, I stratified for 'study' in the model. Like this: <...
1
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1answer
60 views

data storage requirements for RNA-seq and WGS

Supposing upcoming RNA-seq for 3 conditions and 3 replications for each, how much is data storage requirements?
3
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0answers
60 views

How do I prevent the FeatureHeatmap function from the Seurat package, from sorting my data groups in alphabetical order when plotting data?

How can I prevent a function from sorting my data groups (factors) in alphabetical order without affecting the integrity of the data? I am analysing single cell RNA sequencing data using Seurat 2.3.4. ...
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2answers
135 views

Extracting some part of a list

I have two normalized gene expression values (log2 of cpm) ...
1
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0answers
32 views

Circos plot with circlize

This is the post where they made circos using R I'm just following that the part answered by Zuguang Gu, not not sure what I'm doing wrong my file, and the code: ...
3
votes
0answers
43 views

group samples based on shared mutations in a single multi samples vcf file

I am learning about vcf file formatting and sorry for asking a dumb question. I have a multi-sample (>300) vcf file and I want to group (take) samples with shared mutations. Can someone suggest a ...
1
vote
1answer
45 views

Calculating Z-score from logCPM values using edgeR

I have the raw counts for RNA-Seq data. I converted counts data to logCPM using edgeR package. Lets say I have a dataframe A with 15000 genes as rows and 100 ...
3
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0answers
62 views

Several models identify different which genes are significant

I want to find some good predictors (genes). This is my data, log transformed RNA-seq: ...
3
votes
1answer
91 views
1
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0answers
29 views

Complexheatmap update issue

After i updated my complexheatmap library i can;t use my old annotation to label sample this is the image how i used to get something like this Code for the below image ...
-2
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1answer
82 views

Changing this function to work

I have this matrix of expression data ...
2
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0answers
41 views

Ploting FDR along with the pathway as heatmap any simple way

I have this data from one of the cluster which show pathway in context of those genes but when i do a bit of filtering i see plenty of pathways with same or similar FDR which are sort of redundancy i ...
3
votes
1answer
52 views

How to plot genomic.fna fasta file in R using Gviz?

I downloaded the genome of Staph aureus as DNA sequence from NCBI. I would like to visualize it using Gviz. Is Gviz the right tool to visualize genomes? What are the necessary steps from the sequence ...
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0answers
53 views

Making a model of gene contribution in cancer diagnosis

I have raw read counts (Edgeseq technology) of 56 patients who have been ranked with Mandard score as responders and non-responders; I have done differential expression by DESeq2 and I obtained a ...
1
vote
1answer
37 views

Extracting genes differentially expressed by Wilcox test

I have 2 cell types (NOF and CAF) cultures individually and also have been co-cultured with tumour like this picture. https://ibb.co/x8Ty1Wz If this is the log cpm of these 4 samples ...
-2
votes
2answers
38 views

R package installation in r studio [closed]

I have written a package for my personal use and my other colleagues. I have uploaded the files and source package to different websites. I am able to install the source package in my computer. But my ...
2
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2answers
38 views

Using multidimensional scaling to visualize protein sequences by functionality

I have a multiple sequence alignment (MSA) of protein sequences, with which I have performed multidimensional scaling to visualize their clustering. Using R, I used the ...
0
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1answer
60 views

Experimental Design for Differential expreression analysis

I have a Normal esophageal Fibroblasts (NOFs) cultured in DMEM media; The same NOF also have been cultured with a tumor sample from a patient named 005 on DMEM media; I have also Cancer Associated ...
3
votes
3answers
99 views

Kruskal-Wallis rank sum test output confusion

I am running a multiple comparison using the non-parametric Kruskal Wallis test (K-W), using the ggpubr library and I am a bit confused about the results. When i just run the KW-test using "base R" ...
3
votes
2answers
93 views

Separate boxplots for multiple violin plot

I am using the following function from seurat package to generate multiple violon plots and I am interested in adding box plots to them but it doesn't work when I have plotted different data at once. ...
1
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0answers
44 views

R package CMD check errors

I have written some codes in R for my personal use. The package successfully installed on my personal laptop (where I have written those commands) and working correctly. But when I distributed it to ...
1
vote
3answers
62 views

How to obtain amino acid context at a given position

I'm trying to find the amino acid context around a particular position in a protein (5 aa amino acid window on each side). I used to have some code that works and then biomaRt stopped working. I ...
2
votes
1answer
74 views

Extracting genes from corrplot and adding labels based on high and low corelation

I am doing a gene-gene pairwise correlation, I get a plot and I do see positive and negative correlation My code: ...
2
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0answers
64 views

corrplot issue with correlation plot output

Very conceptual doubt not sure if im doing it right or something terribly wrong so im using this corrplot library to calucate the correlation of my desired data frame after that i rounding it off but ...
4
votes
1answer
141 views

How to plot p-values in a circular barplot?

Im trying to plot reactome pathway in for of circular bar plot using ggplot2 my data ...