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.
588
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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
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42 views
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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 ...
2
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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 ...
1
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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? ...
2
votes
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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0answers
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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0answers
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). ...
1
vote
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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0answers
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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0answers
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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votes
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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votes
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(...
1
vote
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 ...
0
votes
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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0answers
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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0answers
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 ...
0
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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:
...
1
vote
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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0answers
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 ...
1
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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 ...
0
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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.
...
1
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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. ...
0
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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.
...
1
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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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0answers
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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0answers
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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0answers
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 ...
1
vote
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 ...
0
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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):
...
1
vote
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 ...
2
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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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vote
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 ...
0
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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 ...
0
votes
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:
...
1
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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 ...
