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.
906
questions
1
vote
1
answer
54
views
stacked barplot with error bars
I need to create a barplot with error bars, my data consists of 2 groups called "Genot", with 3 sub-groups "Suberin" for each, associated with a value "Percent".
...
- 11
2
votes
0
answers
37
views
How to perform liftover from 38 to 37 in R?
I have some gwas summary statistics in GRCh38 that I want to lift to GRCh37. I am trying to liftover in R using this code:
...
- 45
1
vote
1
answer
28
views
PANTHER FUNCTIONAL CLASSIFICATION in R
Does anyone know of a way to programmatically get panther protein class terms and IDs for a gene list, in a way that the classification structure is preserved (PARENT CLASS + CHILD CLASS)?
i.e. For a ...
- 21
0
votes
1
answer
80
views
Statistical approach to link DNA methylation with toxic element exposure and health outcome
I would be thankful to you if you can help with the statistical approach for case-control study to link DNA methylation (epic array) with toxic element exposure (arsenic) and health outcome (...
- 393
0
votes
1
answer
23
views
getting NCBI TAXname by R
I have a data frame on R, called qIns8, with 14 columns and 204 rows. the column called "subject tax id" has NCBI taxIDs for the corresponding row, I need a script to add another column to ...
3
votes
1
answer
36
views
biomarRT conversion of symbols
I wanted to use the code to convert mouse to human symbol, but I have problem with the mirror, I've tried to establish another one, but continue to have the same problem.
...
- 93
-1
votes
0
answers
32
views
1
vote
1
answer
44
views
Intepreting and applying ordinal logistic regression coefficients to calculate probabilities?
Can someone help hint me how I can interpret ordinal logistic regression coefficients and how I can use the .L, .Q and .C terms to calculate probabilities? I am analysing a dataset, where people ...
- 537
-2
votes
3
answers
82
views
Filtering columns from large file based on a column list
I have list of samples as a txt file and want to only keep these samples from this large file; column name is samples name in the large file.
...
- 393
1
vote
1
answer
88
views
Mendelian randomization
I would be thankful to you if you can help with how I can use MR from my case-control study to link DNA methylation (epic array) with toxic element exposure (arsenic) and health outcome (...
- 393
1
vote
0
answers
19
views
DNA methylation mediator analysis for environmental exposure and health outcome
We measured blood DNA methylation using epic array in 100 no-diabetic and 100 type 1 diatbetic patients matched for age, sex and smoking and also measured arsenic exposure using ICP-MS. Could you ...
- 393
1
vote
0
answers
18
views
How to make a POST "vep/:species/region" request that is able to accomodate multiple alternate alleles for a single variant?
There is an R code example on Ensembl's website on how to execute a POST "vep/:species/region" request for variants that only have one alternate allele. The part that holds the variant data ...
- 11
0
votes
0
answers
21
views
Calculating p-value and adjusted p-value for pre-normalized microarray data with fold change precalculated
I have a microarray dataset with two mutants dataset that has already been normalised, and the fold change values for each gene in each mutant versus the wild type have been calculated. I'm interested ...
-1
votes
1
answer
37
views
error in downloading the annotation of sequences on NCBI
I have developed an R function to download the "organism" name of the numerous NCBI accession numbers which are already saved in an object.
The function:
...
1
vote
1
answer
65
views
seeing full results on R
running this code on R, using the Biostrings package,
vmatchPattern("GAAGACCGAGGCCACGCGGAGTACGAACGAGGGTACAGTCTTC", mySeq)
in the console, it writes:
<...
4
votes
1
answer
44
views
How can I incorporate wildcards in Snakemake in an R script?
I am facing the following issue:
I have a rule in Snakemake that looks something like this:
...
- 43
3
votes
1
answer
33
views
How can I export a pruned phylogenetic tree in nexus format in R?
I have a phylogenetic tree with a lot of different populations and I wanted to removes most of them and apply new names to the labels. I wrote this code:
...
- 339
1
vote
2
answers
79
views
Making a DNAStringSet object
I wish to download a fasta sequence from NCBI using "rentrez" package and then save it in an object, then I want to have this object as a DNAStringSet object to work on the sequence using &...
1
vote
0
answers
72
views
Q-Q plots and the genomic inflation factor (k)
I have done the limma association analysis using below model design but not sure how to evaluate Potential systematic biases using Q-Q plots and the genomic inflation factor (k). Could you please ...
- 393
0
votes
1
answer
34
views
A function to produce M fragments of DNA with length of I
I want a script in R, which creates M fragments of DNA with a length of I but with GC content of >70%
I know this gives ...
- 1,981
1
vote
1
answer
24
views
Error importing Maximum Credibility Tree from BEAST into R using treeio's read.beast()
I've encountered an issue that I'm hoping someone can help with. I constructed a phylogenetic tree using BEAST1 and then extracted the Maximum Credibility Tree using treeannotator. I'm trying to ...
0
votes
2
answers
74
views
How to calculate average from a column when consecutive cells are similar in different columns?
I wonder how can I calculate the average of column 7 (WPS_win) when consecutive cells in column 2, column 3, and column 1 are the same. The file is in bed format (tab-separated format). The original ...
- 65
2
votes
2
answers
145
views
How to fix "No gene can be mapped, Expected input gene ID, return NULL..." error in clusterProfiler?
I am trying EnrichKEGG on a few gene samples of genes to check it works before inputting the full genome:
This is my data input as test.csv
...
- 21
4
votes
1
answer
30
views
How to get cytoband and gene level copy number from genome wide SNP array copy number data?
I have (human) Illumina genome wide SNP array copy number data. For each SNP genomewide, I have Log R Ratio (LRR) and B Allele Frequency (BAF).
What tool(s) can I use to get the integer copy numbers (...
- 257
2
votes
0
answers
132
views
How to perform PCA on proteomic data set
I'm trying to perform Principal Component Analysis using R on a proteomics dataset.
As the dataset contains a lot missing values I tried different approaches.
I ran PCA using ...
- 21
3
votes
1
answer
37
views
Why does the subset of rows that match a condition added by the rows that don't match a condition not add up to the total number of rows?
I need to match the external gene names of a table I have called (which has 1,000,000 entries) with their respective ensemble gene IDs.
Here's a small subset of df:
...
- 71
0
votes
0
answers
79
views
What is happening in the Zuker-Algorithm
I am trying to understand the Zuker Algorithm.
What is happening during initialisation? I know in Nussinov the diagonal is filled with 0s. Are the diagonals filled with infinite energy during Zuker´s ...
- 1
2
votes
0
answers
110
views
otu_table from phyloseq object does not have correct abundance: all asv are "0" for specific group of samples
This question was also asked on stack overflow
I have QIIME2 outputs (feature table, tree, taxonomy, and metadata) that I've imported into R using qiime2R (v. 0.99.6) ‘qza_to_phyloseq’ to create a ...
- 121
0
votes
1
answer
29
views
Scale on the y-axis in a tree rotated with 'layout_dendrogram()' using ggtree
I'm editing a time-scaled tree using ggtree. The dates are correctly adjusted when I apply the 'mrsd' command and 'theme_tree2()', but when I try to rotate the tree with 'layout_dendrogram()', the ...
0
votes
1
answer
34
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome
Cross-posted on biostars: https://www.biostars.org/p/9572744/
I am trying to understand better what number to be used and how to put it in the function MRcoefs within the Metagenomeseq package in R ...
-1
votes
1
answer
55
views
What are the fastest way of feature selection in R for large dataset in Machine Learning?
I have about 100 data sets with over 100,000 rows and 27 predictor variables and multiple response variable on each dataset. I want to select the most essential Features for these datasets. I used ...
- 65
-1
votes
1
answer
141
views
1
vote
2
answers
66
views
How to get coefficient tables from multiple regression model result!
I've done multiple regression modeling in R using the below script. Now I'm wondering how can I make a table for the coefficients of each model of all models from lm, glm, and rf separately.
...
- 65
0
votes
1
answer
52
views
Interpretation of clusterProfiler results
I am using clusterProfiler for differential gene expression using this code:
https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html
I have a question about the third line of code:
<...
- 257
2
votes
1
answer
79
views
How to do average macrophages signature boxplots, with Bulk RNA data from 2 control and 2 treatment samples and LM22 signature matrix from cibersort?
I have bulk data from 4 samples of triple negative breast cancer, which 2 of them are control and the other 2 are treated. The goal here is to estimate the average macrophages signatures, for M0,M1 ...
- 101
3
votes
2
answers
124
views
missed cleavages combinations generation
I am looking for an R based solution to the following problem:
Trypsin does not cleave perfectly in proteomics experiments. So starting from a protein sequence FASTA I want to generate all possible ...
0
votes
0
answers
13
views
skip splits in character string [duplicate]
I need to generate a list of sequences from a database, in which a split pattern is skipped up to n-times. As I only know R, I would appreciate an R solution.
Example:
character string:
"GRGKA&...
1
vote
1
answer
59
views
Read methylation data from tar files on GEO (GSE73303)
I'm trying to analyise methylation data using GEO, in order to conduct a multi-omics analysis. The SubSeries I am referring to is GSE73303. Unfortunately, the code used to inspect it produces empty ...
- 41
3
votes
1
answer
79
views
Applying glmnet to identify predictors for subtypes
I am new to glmnet and other ML techniques, so apologise in advance if this sounds a trivial question. However, your guidance is very much appreciated.
So, I have nearly 700 genes with their ...
- 227
1
vote
0
answers
26
views
David tool online not converting most genes
I'm using DAVID tool online, in order to perform functional annotation chart. I extracted the most relevant genes from a dataset (GSE73304), but have the problem that DAVID is not able to understand ...
- 41
2
votes
1
answer
40
views
GEO Methylation dataset "GSE73303" shows 0 features
I'm working for a project using GEO, in order to analyze some gene expression data. The SuperSeries I am referring to is GSE73304, but I found some problems working on the SubSeries GSE73303.
I ...
- 41
0
votes
1
answer
44
views
What kind of data do I need to be able to complete Differential Expression using Limma
I am very new to bioinformatics but have some background in coding with R. I have been asked to find a data set and complete differential expression using the Limma package in R.
I have tried a few ...
- 73
2
votes
1
answer
47
views
Minfi and estimateCellCounts Error: in p[trainingProbes, ]: subscript out of bounds
I would like to plot using estimateCellCounts as I do not know my cell counts for the blood samples I am using however, it seem that I cannot get estimateCellCounts to work with EPIC arrays.
Detailing ...
- 380
2
votes
1
answer
111
views
Help with error DiffBind
This question was also asked on Biostars and the Bioconductor Forum
I want to find differential accessibility between conditions (WS, WF, MS, MF). I can compare any pair conditions without error ...
- 101
1
vote
1
answer
50
views
Gene Set Comparison Without Expression Data
I have been looking all over the web to find some answers to my problem but unfortunately, I was unsuccessful. I wish to determine whether an a priori defined set of genes in my case genes associated ...
- 11
3
votes
1
answer
66
views
Issue with Differential Gene expression analysis with Deseq2
I am using the Deseq2 package to perform a DE analysis on multiple factors.
So, basically to perform the analysis I consider patients characterized by the Brugada Syndrome type 1 and other patients ...
- 31
-2
votes
1
answer
68
views
Assigning multiple GO IDs to an ID: Should I split or use the first or last ID in the hierarchy?
I have a dataset that contains IDs and associated Gene Ontology (GO) IDs. Some of the IDs have multiple GO IDs assigned to them, and I'm unsure how to handle this situation. I would like to determine ...
- 135
0
votes
0
answers
83
views
Gene Ontology (GO) analysis and classification of bacterial whole genome annotations
I am new to Gene Ontology (GO) analysis and would like to classify and visualize the annotations. Here is the background and the steps I have taken so far:
I annotated the bacterial whole genome ...
- 135
-2
votes
1
answer
56
views
Converting a data frame to multiple lists
I have data frame each row is a pathway and it involved genes like
like
...
- 1,981
1
vote
3
answers
243
views
How to join multiple large .tsv (> 20 GB, bed file) files by two identifier?
This question has also been asked on Biostars
I wonder how can I join multiple large .tsv files (over 20 GB each) by using two identifiers (columns) which I used to do using the ...
- 65