Questions tagged [r]

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21 views

comparing two groups using R bar graph

I have two data frames. Let say TissueA and TissueB. I want to compare these two data frames by bar graph in R. ...
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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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21 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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21 views

about the Bray-Curtis distance using 16S rRNA

If we want to calculate Bray-Curtis distance using 16S rRNA, is it better to use normalize counts using DESseq2 and calculate the proportion (normalized counts by total library size) or is it better ...
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21 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
27 views

about the UniProt id and Entrez id

Hi 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
37 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
18 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
35 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
48 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
40 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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21 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
37 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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1answer
28 views

RNA-Seq data transformation prior to sample correlation analysis

If I’m starting with Deseq2 normalized counts what are some preprocessing steps that I should apply to these data before estimating sample correlation using the cor function in R? For example, would ...
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0answers
14 views

Annotation label not matching to the color assigned in complex heatmap

The issue im facing is I'm assignig the colour to the annotation label but when it is rendered the label in my metadata does't match with the final output not sure what exactly is the problem. The ...
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2answers
76 views

Problem with merge data while trying to convert gene names in R

I've been trying to code (in R) a way to convert gene accession numbers to gene names (from RNAseq data). I've looked at all the related questions and tried to modify my code such, but for some reason ...
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22 views

How can I obtain gene lengths programmatically for genes in Wormbase?

I would like to programmatically, in R, obtain gene lengths (excluding introns) of genes of c. elegans given their Wormbase identifier (for example: WBGene00000004). How can I do so?
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41 views

How to aggregate multiple MAF files together?

I have cancer genomic data (tumor/normal whole exome sequencing) from 50 patients that received the same type of treatment, half of whom responded. These come in the form of 50 .maf files, along with ...
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1answer
31 views

Plotting metadata from GenomicRanges object

I have a GRanges object with metadata that I want to plot. Many of the online tutorials which manipulate these GRanges for plotting show how to plot the main columns (chromosome,start/end,strand) but ...
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1answer
40 views

Finding out-group in unrooted tree

Im trying to find the out-group in the alignment my data files file a and file b both the case i'm getting NA when i run this ...
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1answer
33 views

about two group comparison of three group data in DESeq2 package

When we have three groups samples (A,B,C) with 25000 genes and the main interest is A vs B, should we limit samples only A and B for normalization to perform DEG analysis? Or better to include all ...
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0answers
10 views

haplotype network analysis in R

it has been a few days that I am struggling to generate haplotype network analysis for a gene plays important role in pesticide renitence. I am trying a R package "pegas" which seem pretty ...
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1answer
17 views

ERROR: (subscript) logical subscript too long

I am trying to remove a row of a dataframe in R however because the dataframe is so large when I use: rawCounts <- rawCounts[rawCounts != geneID, ] I get the ...
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0answers
6 views

How does one go about developing GCMS metabolite annotation workflow?

I’m really new to untargeted metabolomics and I need to annotate a data set from a standard quadrupole GCMS. The person on the project before me tried to do the annotation manually, cleaning up the ...
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0answers
31 views

merge list of datasets by row IDs in R

I have a list of dataframes with two columns each: $1 = transcript ID, $2 = expression counts (tpm), coming from import of ...
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2answers
30 views

merge rows (to columns) in R dataframe based on IDs

I have a dataframe with two columns: $1 = transcript ID, $2 = expression counts (tpm). This comes from a merging of several ...
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1answer
20 views

Calculating Synonymous and non-synonymous

library(seqinr) library(ape) library(phangorn) alignment file data file sylvia.aln <- read.alignment("abhi_seq/all_seq_no_gal.fas", format="fasta") ...
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1answer
77 views

Which module to select for Pathway analysis based on Module trait correlation and pvalue?

I have a total of 35 tumor samples classified into 4 subtypes. Subtype A, B, C, and D. I have RNAseq data. I'm interested in identifying modules related to each subtype with co-expression network ...
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0answers
43 views

Changing alpha-numeric IDs to numeric only IDs

I need to convert my three text files to the exact formatting of the corresponding example files in order to run my code. I think the formatting error being generated is from the geneID (bold) ...
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1answer
44 views

parsimony and maximum likelihood tree comparison in R

Maximum Likelihood analysis compares the tips or the species based on their sequence similarity while Parsimony analysis compares the characteristic features among the species. So far I did ...
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0answers
16 views

Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data

I am following the tutorial here to learn how to process raw RNA-seq data and get gene read counts. I've had no issues until I got to step 3.9, "Assignment of RNA-Seq Reads to Genes." Here, the ...
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1answer
36 views

WGCNA co-expression network analysis with less than 20 samples

I have two cancer subtypes data. Subtype A is 14 samples and Subtype B is 23 samples. I'm interested in identifying the functions of some LncRNAs in the Subtype A group. For this I'm using all protein-...
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0answers
29 views

exportNetworkToCytoscape in WGCNA in R for a large network

I created a co-expression network for my data using WGCNA in R. I am trying to export my co-expression network into Cytoscape readable format using ...
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1answer
36 views

about the cpm normalization after using normalization factor

Is it okay to use CPM normalization (with/without log transform) after using TMM normalization? Why do we need both? ...
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0answers
45 views

What steps should I follow for DNA analysis, for a classification problem?

I have a bed file which contains DNA sequences information as follow: ** ...
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2answers
35 views

Ranking metric in GSEA

I am using fgsea in r to calculate and plot a bunch of GSEA graphs. My question is whether it is acceptable to use the Wald statistic from DeSeq2 to rank the gene list? I have seen in the GSEA ...
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1answer
54 views

Compare nucleotide mutation with amino acid

To begin with I have two nucleotide sequence to compare I want to see how they might have evolved in terms of sequence similarity and differences. One of the way i can think of is align the sequences. ...
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0answers
23 views

about rescaled data (median) [duplicate]

When we have a rescaled data with median (divided by median value)(e.g.,metabolome) and perform natural log transformation, do we need to use autoscaling again to perform PCA or to compute euclidian ...
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0answers
38 views

about the scaling after normalization and transformation in RNA-seq data

When we use count data in RNA-seq analysis, we usually use normalization and sometimes vst, rlog transformation (DESeq2)or log2(CMP+4) transformation (edgeR) to perform K-means clustering. Can we use ...
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1answer
44 views

How can I plot multiple sequence alignment in R as a heatmap

I have many amino acids sequences in a fasta format that I did multiple sequence alignment. I was trying to plot something like binary a code as heatmap. If it had a change in the AA compared to the ...
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1answer
54 views

Adding external annotation to the phylogeny tree

I was looking to overlay annotation on my phylogeny made,which was solved here question asked where i was looking to compare two different phylogeny which i could do. Now i want to label the tips ...
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1answer
34 views

Very low probability densities

I'm generating a density plot using the ggplot2 library: ...
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4answers
168 views

Comparing phylogeny in R

So I want to compare the phylogeny created using two methods for example Maximum likelihood and maximum parsimony.Is there any way to compare the two phylogeny ? I did read about phangorn but not ...
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0answers
17 views

Convert Data to be suitable for M3Drop did not work

When I try to convert data to use with M3Drop, I get the error message shown below. Does anyone know the reason and how to deal with it? Thanks! ...
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1answer
37 views

PCA plot did not work in single cell RNA-seq

I run plotPCA for single cell RNA-seq data, while I get error message (I use R 4.0). I attached the code and error message here. Did anyone know the reason and how to deal with it. Thanks! ...
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1answer
88 views

calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics

I am trying to follow a tutorial from Sanger institute (from May 2019) on analysis of single cell RNA Seq data. They use calculateQCMetric function to calculate the quality metrics, but I am getting ...
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2answers
61 views

Selecting rows by partial match

I have a data frame one column is sample name like ...
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1answer
29 views

How to remove zero value of gene on FeatureScatter plot using Seurat?

Nowadays, I am trying to calculate Pearson correlation values between two genes of my interest from single-cell RNA-data (features.tsv, barcodes.tsv, and matrix.mtx files) which are obtained from the ...
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1answer
17 views

phangorn fasta file read error

Im trying to read a multifasta sequence file into phangorn I get the following error ...

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