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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14 views

Bioconductor, genefilter() returns NULL dimensions, is my filtering process wrong?

I'm using R and bioconductor in order to conduct some gene analysis on an Affymetrix dataset (GSE173360) but I'm having trouble at filtering genes. I'm trying to create a dataset called small.eset by ...
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What are the best practices for comparing .seg copy number outputs from iChorCNA to VisCapCancer?

I have shallow whole genome sequence data that I used the tool iChorCNA to find the mean copy number segmentation per region. The tool produces a seg file and can be seen here: https://github.com/...
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0answers
80 views

How do I create a horizontal stacked bar plot in R? [closed]

I have the frequency of four chains in T cells : alpha chain (TRA), beta chain (TRB), delta chain (TRD) and gamma chain (TRG) I have five patients ...
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1answer
35 views

How to increase the size of the shapes that denotes effect sizes of different datasets and metaanalysis?

I am doing metaanalysis with forestplot from ggforestplot package. I have 7 different datasets from 7 different countries. After metaanalysis, I have 7 Effect sizes and a Meta-analysis effect size, i....
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0answers
24 views

seqff script got trouble after samtools treatment

I'm trying to study fetal fraction by using a seqff script from here. The instruction says that I need a headless sam file to work so after alignment with bwa, I process my sam file by using samtools: ...
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1answer
30 views

Clustering with Seurat

My data consists of two groups control and stim. I'm concerned that my clustering in the stim group is dominated by the unregulated genes. I can remove these genes and recluster but is there a way to ...
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1answer
57 views

how to sort and join two files based on First Column Id

I have got two files large files like this in Tab-delimited format, trying to merge in R, do we need to sort the file before merging? ...
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1answer
29 views

correlation coefficient versus DEGs analysis: what's the best approach for low expressed genes?

I have 6 folders. Each one contains 7 datasets of a specific type of cancer (RNA-Seq) and 7 datasets of normal tissue (healthy control for that type of cancer). A total of 84 datasets. I want to ...
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0answers
24 views

Data format for pathway based clustering of samples

I came across this paper as one of the examples from this paper, this one Figure 2. Host Protein Alterations in Infected iAT2s ...
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1answer
26 views

Toptable error, wont recognize condition

I am getting a rather strange error from topTable. When I run my code I get Error in fit$coefficients[, coef] : subscript out of bounds from topTable as if it is ...
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1answer
28 views

Annotating gene names or gene IDs to a dataframe containing SNPs?

I have a large data-frame (excel file) of SNPs with genotyping data. I need to filter the data to get SNP information of a specific gene alone. The list is too long to do it manually. I was wondering ...
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1answer
33 views

Common gene naming conventions and how to convert between them

I have two questions, one is a direct question about some RNA expression data. The other is more broad, but motivated by the first. I have downloaded an expression set for a class project and I am ...
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1answer
45 views

Determining what RNAseq data is filtered on volcano plot

I am using RNA seq data to analyze genes via a volcano plot comparing differential gene expression of bacteria with and without antibiotic in R. After having created my plot, I am unsure why some of ...
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1answer
19 views

How to extract column from a matrix matching the another file (sample file)

I have two files master file.txt and sample.txt master.txt ...
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1answer
26 views

Calling GEOquerry error while loading the library

I started getting a strange error when trying to load GEOquerry with library(GEOquerry). ...
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1answer
23 views

Brackets in .Rmd code blocks

I am making some R markdown documents for my stats class. I've noticed I get an error in some functions when I have a code block with {r} instead of just r. Like so... ...
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1answer
19 views

How to import a phylogenetic tree (in nexus format) with node support values in R

I have a phylogenetic tree in nexus format that was generated with RAxML. In the tree file, there are node support values. I want to plot this tree in R with the support values showing. However, when ...
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1answer
21 views

Create a NHX phylogeny format with r or python

I need help to add information in my phylogenetic tree on each branch. I have two pieces of information at my disposal: 1 ) A phylogenetic tree in newick format : <...
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1answer
33 views

genotyping or variant calling in R

Are there any good options for calling variants or even just a pileup from R? R is not ideal for this, but I'd like to integrate with other functions. I found deepSNV::bam2R which roughly does what I ...
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1answer
26 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
30 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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0answers
23 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 ...
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1answer
80 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
18 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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0answers
24 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
32 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
66 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
48 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
38 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
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1answer
53 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
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1answer
85 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
31 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
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1answer
48 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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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 ...
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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
16 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 ...
1
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1answer
56 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
25 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 ...
1
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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 ...
0
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1answer
43 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 ...
1
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1answer
48 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
74 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
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2answers
50 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
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1answer
61 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
86 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
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1answer
42 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
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1answer
47 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
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2answers
59 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
43 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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