Questions tagged [r]

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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 ...
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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 ...
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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 ...
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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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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) ...
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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 ...
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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 ...
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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]...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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
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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 ...
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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 ...
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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 ...
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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
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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
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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 ...
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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 ...
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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
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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: ...
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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 ...
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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: ...
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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
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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 : ...
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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 ...
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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 ...
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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
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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?
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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 ...
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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 ...
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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
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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
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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? ...
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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
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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
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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 ...
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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 ...
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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
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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
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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)...
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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
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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
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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. ...

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