Questions tagged [r]

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20 views

SeqFF for estimating freaction Error

I am beginning with bioinformatic genomic. I am very interested in NIPT. I use SeqFF.R package for estimating fetal fraction. I downloaded seqff.R package in https://obgyn.onlinelibrary.wiley.com/doi/...
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1answer
23 views

Add segregating sites to branches of a tree

I'm trying to figure out how I would plot a tree with number of segregating sites on display on the branches I'm using acctran from phangorn to plot a parsimony tree (using phydat object from fasta ...
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1answer
88 views

Find intersection among multiple columns and find the intersected elements [closed]

file input file ...
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42 views

Help importing a biom file into R

How can I import a biom file? When I run the following code: ...
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25 views

Standard Way to Preprocess Gene Expression?

I am trying to collect gene expression data for the point of fitting gene regulatory networks. My background is primarily in computer science and so I am finding the biological literature a bit ...
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2answers
37 views

How to refine this distribution comparison script

My data look like this They are compound similarity estimations(the whole file is around 10GB). What I am trying to achieve is to compare the similarity distributions of each compound using the ...
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1answer
32 views

DESeq2 - Error in lfcShrink: 'coef' should specify same coefficient as in results 'res'

I have created a DESeq object (dds) and now I want to access the results and apply the lfc shrinkage on them. ...
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2answers
85 views

FPKM, FPKM-UQ, TPM or counts: How do I know which kind of unit should I use?

I'm trying to download data from the TCGA for gene expression analyses in R, but I'm in doubt if I should use FPKM, FPKM-UQ or counts? When the dataset is in counts, I suppose it's raw data, isn't it? ...
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1answer
44 views

Microarray Meta-Analysis and Cross-Platform

I have a microarray dataset with Agilent platform, all of the samples are cancerous, I need normal or control samples to compare with cancerous samples, can I combine control samples from another ...
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1answer
42 views

Error When Using biocLite as an installer in rpy2 python library

I am running into an error when I tried to run the following lines of code, the error at line 3: ...
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14 views

I do not understand the output of ssGSEA using GSVA package in R

I am using the GSVA package in R to do single sample gene set enrichment analysis (ssgsea) using method = ssgsea. This works, ...
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18 views

Retrieve ATC codes for New Clinical Trials

I have a STATA list of 4000 medicinals used in clinical trials and need to associate an ATC to them. I have scraped wikipedia and BBPharma website and found out some ATCs (missing and None included). ...
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1answer
73 views

Python equivalent to R GRanges and IRanges

Problem: I am trying to convert some codes written in R to Python and part of that conversion process is find classes equivalent to the GRanges and IRanges from the GenomicRanges R package in Python. ...
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26 views

workaround for error: Bad CPU type in executable c

I use clustal() from library ape every now and then, but now it doesnt work... code: sylvia.clus = clustal(sylvia.seq) Error: ...
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24 views

About getting rs id from chromosome and position

Hi I have a dataset with chromosome and position. VARIANT_ID chromosome position 17_26797415_147499 17 26797415 17_26797556_147500 17 26797556 How can I ...
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1answer
45 views

Making a union data from different list of genes

I have two groups of patients I have a list of driver genes Clearly each group have mutation in a subset of these gene some of which are common between two groups and some of which are unique to one ...
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1answer
45 views

About the log2 fold change

Hi I have a basic question. It seems that we have two calculations of log fold change. Actual log2(FC) = log2(mean(Group1)/mean(Group2)) Limma's "Log(FC)" = mean(log2(Group1)) - mean(log2(...
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1answer
49 views

TCGA: gene IDs not appearing and other concerns

I want to download RNA-seq datasets of 4 or 5 different types of cancer from the TCGA to investigate what is happening with my gene of interest. The problem is that I'm a physician and I don't know ...
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1answer
52 views

Parsing the json file from gene ontology result into dataframe

How do I parse the json file from ontology output. My file json file jdata <- read_json("analysis.json", simplifyVector = TRUE) I want to convert it ...
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57 views

Adding legend to Botton and top annotation in complexheatmap

I have a heat map but top and bottom annotation don't have legend ...
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1answer
25 views

Unable to use phangorn::phyDat

I am following an example from ‘Analysis of Phylogenetics Second Edition and Evolution with R’ from Emmanuel Paradis. He is doing: I am doing pretty much the same: ...
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15 views

Questions about EBSeq (in R)

I have made a UMAP of malignant cells and the result is split into 3 clusters, as seen below. For the sake of example, let's say I want to find the differentially expressed genes in the uppermost ...
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1answer
61 views

Interpreting this plot from GSEA

I have RNA-seq for two groups of patients: Responders to chemotherapy (n=9) versus ...
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1answer
20 views

Error running GenomicVis vcf.venn(vcf.files, 'GRCh38', sample.names)

I am trying to draw venn diagrams with a GenomicVis package (R). library(GenomicVis) It is loaded with a warining: ...
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1answer
83 views

Seurat FindMarkers() output interpretation

I am using FindMarkers() between 2 groups of cells, my results are listed but i'm having hard time in choosing the right markers. Do I choose according to both the p-values or just one of them? If one ...
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22 views

About the Bray-Curtis distance

If we want to calculate Bray-Curtis distance, is it better to use normalize counts using DESseq2 and calculate the proportion (normalized counts by total library size) or is it better to use raw ...
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1answer
40 views

Differentially expressed genes analysis in Seurat

For the differentially expressed genes analysis, is it possible to check for DEGs based on the levels already identified in the object? For example, my dataset contains cells from 11 subjects, which ...
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0answers
29 views

How to implement SEG (Wootton and Federhen ,1993) algorithm?

I want to implement SEG in my MATLAB environment and I'm relying on Wootton and Federhen (1993) Reading the article I cannot succeed to understand what kind of process I have to implement in order to ...
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1answer
33 views

Changing active.ident in Seurat

Im trying to change the active.ident to another column in metadata but this error keeps popping up! I recently upgraded to R version 4.0.2 from 3.6.1 The older version was working but the new one isn'...
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2answers
62 views

can I download DESeq2 in R 3.6.3 in Linux MInt?

I am trying to download DESeq2 in R 3.6.3. Is it possible? This is printed when I am trying: Warning in install.packages : package ‘DESeq2’ is not available (for R version 3.6.3) Thank you!
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1answer
50 views

europmc and tidypmc R library for extracting or making metadata from publication

I'm trying to use this europmc r libray where I have a list of pmids to look for. I tried with pubtator but its bit complicated.In Europmc i can all the annotated terms etc. ...
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2answers
34 views

no result from heat map WGCNA

I have created a heat map using WGCNA using R. But the heat map command is not showing the plot and there is no error. I have a large number of modules and traits. I am not sure if that is the reason. ...
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2answers
82 views

Subsetting from seurat object based on orig.ident?

I am pretty new to Seurat. I want to subset from my original seurat object (BC3) meta.data based on orig.ident. however, when i use subset(), it returns with Error. ...
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2answers
35 views

How to fit all genes (labels) in chromosome ideogram plot made by RCircos package?

I am using Rcircos to make a chromosome ideogram plot for my gene list (n = 45). However, I am getting this error: ...
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25 views

Meta-analysis and data curation tools in R

I'm looking to run meta analysis. First step is data curation. How exactly data curation for metanalysis is done? I did a few searches which gave me some lead how to start. This is one of the tool ...
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54 views

How to use seqff for estimating fetal fraction

I downloaded seqff package here, but I don't know how to use it properly. I have some fastq files generated by Illumina machine, I want to analyze them, as I understood, I have to convert them to ...
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0answers
60 views

Kraken2 or metaphlan2 report to phyloseq

I wish to convert a kraken2 or metaphlan2 report into the R package to analyze using Phyloseq. I have performed obtained an importation and Phyloseq analysis, but the result was not correct. ...
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1answer
49 views

maftools tcgaCompare plot: x-axis labels getting clipped

I have a {maftools} plot: whatever I try to save that completely I see the down part of plot is trimmed like I have tried both save as pdf and save as image options which did not differ Any ...
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13 views

Identifying substrates with enriched degradation potential from count data of enzymes able to degrade that substrate across all samples

How would I identify if I have enriched degradation of a certain substrate within a clade of bacteria with count data of enzyme capable of degrading a range of substrates? I have started of by ...
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0answers
39 views

Non-finite value supplied by optim in Hurdle model of enzyme count data

I have a dataset of enzymes counts that are grouped by substrate they degrade and am attempting to model if the origin of the genome in which the enzymes were found can predict the count for ...
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1answer
44 views

Comparing aligned amino acids to codon

I have a set of 4 amino acids which i have aligned,but i want to compare then with respective nucleotide sequence in terms of change codon level. I have the alignment file where i want to take only ...
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1answer
39 views

Mapping UniProt id to Entrez id

How can we get mapping from UniProt id to Entrez ID? I have UniProt id, but want to convert those ids to Entrez or Ensembl id.
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2answers
42 views

What does aov(glm model) actually do in R?

What is happening when you use aov() on a glm model in R? Normal glm model sumamry(m1): ...
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1answer
21 views

classifying samples by TCGA signature

I have some RNA-seq samples from multiple glioblastoma tumours that I'm now trying to classify according to a specific gene signature (from Verhaak et al., 2010) using R. The gene signature is ...
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0answers
58 views

How to calculate module-trait relationship when trait data is in binary format?

I have a dataset of 50 breast cancer samples. These samples are classified into four subtypes Lum A, Lum B, Her2 and Basal. I have been working with lncRNAs and protein-coding genes. To identify the ...
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2answers
73 views

How to create a list of differentially expressed (DE) genes after normalization with RUVSeq?

I am using edgeR to perform differential expression (DE) analysis on a set of RNA-seq data samples (2 controls; 8 treatments). To correct for batch effects, I am using RUVSeq. I am able to get a list ...
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1answer
38 views

how to extract a different substring for each row of a dataframe in R?

I have a dataframe with putative alignments of thousands of probe sequences. I would like to pull out the adjacent nucleotide from the genome for each alignment. My dataframe includes ...
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1answer
47 views

R not being able to find the file despite being in correct directory

I have question regarding a project I have to do about a health student study. I cannot import the csv file via read.csv or read.csv2 despite having transformed all files to csv and being in the ...
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0answers
29 views

Calculate Entropy for DNA Multiple Sequence Alignment in R

I am pretty new to R. So I apologize for asking maybe a very basic question. Let's say I have a fasta file with sequence below: ...
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1answer
43 views

How do I set a neural network to loop multiple times and average the resulting values?

I have a script in R/RStudio which creates random datasets of binomial variables, feeds them through a neural network, and calculates their likelihood ratio statistic and deviance. I'd like the script ...

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