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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
43 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?
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0answers
33 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
116 views

Extracting some part of a list

I have two normalized gene expression values (log2 of cpm) ...
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0answers
14 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: ...
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0answers
37 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 ...
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1answer
37 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 ...
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0answers
52 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: ...
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1answer
69 views
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0answers
17 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 ...
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1answer
76 views

Changing this function to work

I have this matrix of expression data ...
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0answers
29 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
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1answer
43 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
50 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
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1answer
29 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 ...
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2answers
35 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 ...
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2answers
31 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 ...
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1answer
59 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 ...
2
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3answers
74 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" ...
2
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2answers
56 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. ...
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0answers
31 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 ...
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3answers
60 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
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1answer
51 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: ...
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0answers
31 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
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1answer
93 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 ...
2
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0answers
22 views

R package grur: missing_visualization() fails during redundancy analysis of .vcf

I am trying to use the R package grur to process GBS SNP data, which is installed from github as instructed. For starters, I am running the test code in this vignette. As suggested I am running it ...
3
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0answers
45 views

SingleCellExperiment: invalid rownames length

I did all of the installations from scratch in a virtual conda environment. Then I tried to run R script from within ...
3
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1answer
47 views

Subset data frame based on ID

I tried to subset the dataframe in R since there are empty space after each line in the sequence which shows 'NA' when i read the files into R ,as a result of which when i subset it just takes the ...
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2answers
44 views

Why the t-test for a specific gene shows different value compared to differential analysis?

I have RNA-Seq data for LUNG cancer. 370 tumor and 50 Normal. For differential analysis initially I did some filtering and kept approx. 19k genes for further analysis. I used edgeR. With a FC > or &...
1
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1answer
54 views

Creating a computational table to show the number of available genes between all possible pairs of combinations in eight gene lists

I am looking to create a table (on RStudio) that will show the overlap between 8 different gene lists wherever possible. I have saved the 8 lists as .txt files all in one folder and set that ...
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0answers
35 views

How to plot gene mutation frequencey in terms of percnatge alteration in samples?

I'm taking data from cbioportal of gene and their mutation frequency with percentage which I'm trying to categorize with various sub class. The issue I'm facing is I have to plot it in mutation ...
2
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1answer
43 views

Question about the dots on Quartile groups in boxplot

I have Microarray Normalized Expression data for a specific Gene. It looks like below in a dataframe B ...
2
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2answers
117 views

Using Seurat to compare mutant vs.wt

I am interested in using Seurat to compare wild type vs Mutant. I don't know how to use the package. How can I test whether mutant mice, that have deleted gene, cluster together?
2
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1answer
58 views

ScaleData() from Seurat causes crash on RStudio Cloud

Using the sample data in the 2,700 PBMC clustering tutorial, the session crashes at the ScaleData() step. The progress bar remains at 0% and hangs, followed by an R ...
3
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1answer
40 views

different results coming from biomart online and biomaRt R library

I am playing with biomart in order to get the list of genes associated to a specific gene ontology (GO) term. So, if I use the webservice as in this query: I get at least 50 genes. If I download the ...
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2answers
91 views

Multiple correlation with R

I have a data frame presenting different variables in column and for different species name in rows as follow. In the column a have only one independent variables(Proteome size) and all the others are ...
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3answers
57 views

How to convert data in gmt format to dataframe?

I downloaded c5: gene ontology gene sets file from http://software.broadinstitute.org/gsea/downloads.jsp I opened the "c5.all.v6.2.symbols.gmt" file in csv format and It looks like below: I want to ...
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2answers
26 views

levels of factors in the design have non-unique level names after make.names() is applied

When I try to import the data using DESeq2 package: dds <- DESeqDataSetFromTximport(txi, sampleTable, ~Group + Cre) I am ...
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0answers
76 views

GO Term heatmap plot in terms of P value or fold enrichment

I'm clustering genes in terms of expression after clustering them. I'm taking out clusters and trying to find out what kind of GO terms are coming up. I came across this figure from this paper, I want ...
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1answer
49 views

How to get the corrected matrix after SVA batch effect correction

I ran SVA to remove batch effects for my bulk RNAseq experiments, but now I need to somehow correct my data matrix in order to ...
2
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2answers
103 views

Changing a wide range of colours to a limited gradient

I returned a FeaturePlot from Seurat to ggplot. My plot has a weird range of colours as below I produced this plot by this code ...
2
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1answer
96 views

3D PCA group labelling

I would like to make a 3D PCA but not sure how to label group wise which i can do for 2D PCA ...
2
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1answer
55 views

How to transform a DNAStringSet from the Bioconductor package Biostrings to a data frame?

I am working on Mac OS X. I am using R version 3.5.1. I have important a FASTA file into R using Biostrings::readDNAStringSet. This creates a DNAStringSet object ...
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0answers
32 views

Bioconductor, how to retrieve the genes from a GEO gene expression dataset?

I'm quite new to Bioconductor and GEO. Here's my task: I've to develop a simple R script able to read a gene expression dataset on GEO and extract the genes related to it. But... I don't know the ...
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2answers
64 views

How to deal with duplicate genes having different expression values?

I have RNA-Seq data which is FPKM. In the dataframe df first column is gene_name and the ...
3
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1answer
48 views

RSVSim insertions from chr1 to chr2

edit explaining python tag I would still rather have a solution based on the RSVSim package in R, but while waiting for someone who might have an answer I wanted to look at other solutions as well. ...
3
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1answer
42 views

about dotplot legend meaning

Here is the code I used: ...
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1answer
98 views

Converting Gene Symbol to Ensembl ID in R

I'm trying to convert ~20,000 different human gene symbols to ensembl IDs. I've been trying to use biomaRt to do this, but continue getting the following error ...
4
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3answers
222 views

Script to allow gene set enrichment analysis of 10x genomics data in R

I have 10x single cell RNA seq data. Which R package is best suited for analysis of the 10x data matrix. What is the script to prepare the data for downstream GSEA analysis. I have already processed ...
4
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1answer
46 views

Why are my Chi-squared test results different from those in a published table?

I recently read the paper “A novel long non-coding RNA linc-ZNF469-3 promotes lung metastasis through miR-574-5p-ZEB1 axis in triple negative breast cancer”. In this I see Table1 showing correlation ...
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0answers
77 views

How can I read multiple different regions from a BAM file?

I’m trying to process BAM records (of a coordinate-sorted, indexed BAM file) successively in fixed-size, non-overlapping, sliding genome coordinate windows. Unfortunately I am unable to read records ...