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.
630
questions
0
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0answers
13 views
About optimal distance (or dissimilarity) measure in proportion data
If we would like to use data with proportion (e.g.,total sum scaling or compositional data), what kinds of distance or dissimilarity can we use?
Bray-Curtis is one of them, but does this make sense to ...
0
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1answer
19 views
STRINGdb: reverse map STRING identifiers to gene names?
Is there a functionality within STRINGdb package or in another environment to reverse map the STRING identifiers to Gene names?
For example, the entire STRING network can be downloaded using the ...
0
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0answers
22 views
multi--platform GEO analysis based in expression of single gene
I have a challenge in analyzing GSE34941( It has 4 platforms) according to the expression of a specific gene in R. First, which is the best way to group my patients according to the expression of a ...
-1
votes
1answer
74 views
Multiple box plot
I am using below code to plot multiple box plot but I am still struggling to understand how I can add whisker to box plot and how to change sample order like in this figure SampleType?
...
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0answers
16 views
How to retreive all the genes belonging to one GO term
I'd like to retreive all the genes belonging to a GO term.
I tried (in R):
library(org.Hs.eg.db)
xx <- as.list(org.Hs.egGO2ALLEGS)
...
0
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0answers
23 views
How can I retreive specific qualifiers from genbank files in R?
I'm trying to extract the host field from the features table using the biofiles package. From what I understand, the function filter (from the same package) could be of help but I can't extract the ...
1
vote
0answers
17 views
How do I include silent mutations in an oncoplot using maftools?
I have annotated files from annvar and I changed them into MAF by using
annovarToMaf from ‘maftools’. Then I used read.maf to ...
0
votes
1answer
36 views
Error in if (is.na(sra_acc$run[i])) { : argument is of length zero
I am trying to write a code for importing sra files as fastq files in Rstudio (for obtaining and aligning RNA-seq reads from public repositories). I keep getting "Error in if (is.na(sra_acc$run[i]...
2
votes
2answers
30 views
how to easily make complex Euler/Venn diagrams in R?
From my microarray data I have selected three subsets of probes. I would like to display these subsets as a Euler diagram to visualize the overlaps, but am struggling with inputting the combinations ...
1
vote
1answer
37 views
Retrieve overlap widths with Bioconductor
I want to retrieve all overlaps between two sets of genomic intervals (GRanges) using Bioconductor. I am interested in the widths of the resulting overlapping ranges.
In cases with discontinuous ...
0
votes
1answer
41 views
Regarding canonical analysis of principal coordinates (CAP) for linking microbial data with elements
I used the below code to do CAP analysis to link microbial data with elements, but not sure how to do statistical analysis to show which element variation is responsible most for the difference in ...
1
vote
0answers
39 views
Confirmation about PERMANOVA and Variance partitioning (permutest)
Could you please help me to understand what is the difference between Permutational multivariate analysis of variance (PERMANOVA,adonis) and Variance partitioning
(permutest).
I understood that ...
1
vote
0answers
28 views
workflow for processed RNAseq data analysis in R [closed]
I'm learning to use R in data analysis. I'm getting fluent in baseR and the tidyverse, but thus far only dealt with medium throughput plate-based experiments.
I am currently trying to learn how to ...
0
votes
1answer
34 views
RNA_Seq Analysis in R, propmapped function issue
I'm currently trying to learn RNA-seq data analysis and differential expression in R. I've been using the Combine lab tutorial.
Everything was running well until the tutorial asked to use the ...
0
votes
0answers
9 views
How to assign LD proxy
When we use local data using TwoSampleMR, how can we assign LD proxies where the outcome data is not available?
https://mrcieu.github.io/TwoSampleMR/articles/outcome.html
...
0
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0answers
53 views
Adding matrix as a confounder in EnrichmentBrowser
Brain data, particualrly human brain data have very heterogeneus cell types, so it's important to normalise by cell type/add proportoins of different cell types to the formula when performing ...
1
vote
0answers
19 views
Generate multiple output file based on editing operations done on PDB input files stored in same directory
I have hundred PDB files that I want to loop through in the directory and carry out some editing operations and save them as new PDB files using R script. Right now, I am using the following code but ...
1
vote
0answers
14 views
how can I condense this forest plot to a single line?
I am doing meta-analysis with around 100 dependent variables by metafor package. I want to plot the effect size and random effect in a forest plot. For that, I am following a tutorial where it has ...
2
votes
1answer
54 views
How to write multi-sequence alignment data frame as a fasta format fast
I have a data frame where the row names are the species names, and each column can either be an Amino-Acid character or "-".
I wish to write it in a fasta format. Simple example of the ...
1
vote
0answers
20 views
FastqCleaner in R, not recognizing paired-end fastq file?
I've recently downloaded the FastqCLeaner to process paired-end fastq files locally using R (4.0.3). I'm having trouble with the shiny app. It is not uploading my second fastq file, and is repeated ...
2
votes
0answers
25 views
What is the best way to start for analysing DNA methylation TGCA datasets using R? I want to learn but I'm a novice
I am relatively new to programming and only have a basic knowledge base for R. I am keen on learning how to manipulate DNA methylation arrays for analysis related to Glioblastoma Multiforme. More ...
1
vote
1answer
41 views
How to select specific lines and specific columns
Please I'm a beginner in using R and I work on database.
I have a database that contain lot of columns and lines, like this for example
...
2
votes
1answer
39 views
ggplot2 geom_bar() , do not merge y-values shared same x-ids [closed]
I am plotting a barplot using ggplot + geom_bar() function in R.
I have some the recoreds which share the same x-axis ...
3
votes
1answer
64 views
the model matrix is not full rank : This is a classic question which a biologist face without clear understanding of the model design
Saw this answer biostar. Tried to make my metadata as such but still the
"Error in checkFullRank(modelMatrix) : "
This is my coldata
...
2
votes
2answers
38 views
ATAC seq peak annotation : Which peak to choose for downstream analysis
After doing peak call I'm annotating the peaks using chipseeker tool, which I want to take further downstream analysis. Now unlike RNA seq where i have single gene and their respective expression. But ...
-4
votes
1answer
57 views
Summing up one column entries for each sample [closed]
I have a dataframe with 27 samples and for each of them I have different number of values
I want to sum up the values for each sample, leaving each sample with a single value
...
2
votes
1answer
69 views
shiny code with seurat object
I am trying to create a shiny board for my scRNA seq data. I have saved my seurat objects adn I use following code as below:
...
1
vote
1answer
36 views
how to train a gene dataset with a nearest shrunken centroid classifier?
I have a data file named "geneexp.csv".
the data contains information about gene expression of three different cell types (CD4 and CD8, CD19) I want to classify cells by performing the ...
1
vote
1answer
44 views
How to calculate RNA copies in qPCR using R?
I have these Ct data from qPCR for a series of samples A-H, I want to quantify the RNA copies of my samples using R:
...
0
votes
2answers
56 views
How would we test for significant changes in expression when many of the normalised counts are clustered together?
I've been handed RNA-seq data with a lot of associated covariates.
This data has been put through the DESeq2 package and as a result normalised the data.
One of the transcripts of interest still has ...
2
votes
1answer
38 views
Plot information stored in dataframe within a tree (ggtree)
Hello to the entire Stackoverflow community!
I'm writing to you because I'm currently building a phylogeny with ggtree and I have in parallel a table like this one:
df :
...
0
votes
0answers
20 views
Get dataframe from an LipidomicsExperiment when using lipidr package
With the library lipidr lipidomics data has been normalized using the function normalize_pqn(), and I need to get the normalized data to perform further statistical ...
0
votes
0answers
17 views
How to analyze the correlation of two different tissue gene expression under three conditions?
I have three conditions A, B, and C. For each state, I have gene expression data of two different tissues(liver and pancreas). I am studying the possible network/correlation/ between tissues for each ...
0
votes
1answer
21 views
Extracting concatenated metadata from a column in R
I've downloaded some ChIP-seq data from www.chip-atlas.org and I want to use this to conduct some enrichment tests with genomic regions from my experiment. The .bed file generated by that website is ...
3
votes
1answer
35 views
Extracting p-values using corrr package in R
I'm performing correlation analysis using the corrr package in R, but I'm unable to extract the p values. Does anyone know how to get the p values in corrr package in R?
2
votes
0answers
15 views
co-expression analysis for two different tissues of same sample
I have gene expression datasets A and B that contain as many rows as genes and as many columns as samples. The rows in A and B represent a common set of genes measured in different tissues of the same ...
1
vote
0answers
42 views
Meta-analysis in R [closed]
I am completely new to meta-analysis and am a bit lost on how to proceed.
I have two biomarker datasets; each one is using a different microarray platform. I have the protein names, the concentration ...
0
votes
1answer
84 views
DESEQ2:Error in rownames, what is the problem?
I am using DESEQ2 for RNAseq analysis but i do not understand why I get this error.
...
3
votes
4answers
119 views
I have really skewed RNA-seq data, what's the best way to normalise it? Preferably in R!
My data frame compares the RNA-seq reads from many genes in different tissues.
The reads look as follows.
I tried using log to make it better but still looks pretty skewed.
Are there any better ...
1
vote
1answer
31 views
How to download sequence alignments against UniProtKB sequence database for a particular Pfam Id using R?
I am trying to download sequence alignments for families against the UniProtKB sequence database as shown in the example below using R code. Can someone kindly suggest me how to?
...
1
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0answers
13 views
How to use EPIC DNAm files (.idat) to infer copy number alteration
I have access to EPIC DNA methylation profiles from approximately 40 samples. I want to use these .idat files in order to predict copy number alterations within specific promoter regions of interest. ...
0
votes
1answer
34 views
Table error when combining counts columns
I have these files that I want to make table of (https://github.com/learnseq/RNAseqfiles01.git), the table that I want (since all the files have the same ID column),, I want merge the ID column with ...
1
vote
1answer
42 views
Splitting data table up based on separate file of gene names
I am very new so bare with me. I have a file called data (.csv that I turned into a data table) with 2 columns (geneid, normalized counts) and about 9000 rows. I have a second file called Xgenes of ...
0
votes
1answer
19 views
Error in cor(exprs(gse), use = “c”) : no complete element pairs
I'm trying to plot a heat map for a "GSE133399", I retrieved the GSE using GEOquery package and then assigned to an object and then tried to plot a heatmap, but I was not successful, I used ...
0
votes
2answers
56 views
Why is Mann-Whitney U-Test over an ExpressionSet yielding different results than original paper
I am trying to replicate the results of this paper roughly guided by this pipeline.
Basically, we are trying to detect a differential expression between mesenchymal and epithelial cells under ...
0
votes
0answers
42 views
tissue cross talk using gene expression data
I am studying about tissue cross-talk using gene expression data. My first goal is to identify the genes responsible for communication signaling(cross talk). Let say the tissues are fat and muscle.
...
1
vote
1answer
58 views
error in random forest analysis
I am now struggling to do random forest analysis, I will be thankful if you could help with code for random forest analysis.
I got samples from the root, soil, and leaf from two regions (bau & mau)...
-1
votes
1answer
65 views
Too slow issue of BioMart
I am using library(biomaRt) in R to annotate SNP rsid. It takes too much time for only 1000 SNPs....... I would like to know how I can run this code faster.
...
1
vote
1answer
37 views
gene-gene correlation from two different Tissues
I am stuck on how to do correlation for two independent data sets with common row and column names.
A and B are datasets that contain as many rows as genes and as many columns as samples.
The rows in ...
0
votes
1answer
49 views
alpha diversity wilcox.test
I am trying to do Wilcox test to detect the significant difference in alpha diversity but it is showing an error? physeqN2 is a phyloseq object and Season is a metadata column.
...
