Questions tagged [r]

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how to create "sample file" for the qAlign() function after trimming the reads in R

I'm an absolute beginner trying to solve this question "Align the trimmed and untrimmed reads using QuasR and plot alignment statistics, did the trimming improve alignments?" I did trim the ...
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1 vote
1 answer
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Association analysis for methylation beta value and phenotypes in R

I am trying to learn how to do association analysis of methylation array data with numerical trait like body weight, eGFR. As I have seen some of the publications, methylation data association with ...
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What is the difference between AnnotationDbi/org.Mm.eg.db and biomaRt/Mus.musculus for converting to gene symbols?

I am interested in the differences between AnnotationDbi/org.Mm.eg.db and biomaRt/Mus.musculus. They yield the same results as seen in the code below. ...
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Cytoscape for coloring the nodes in the network

I need to color different categories of the proteins in the interaction network automatically. Is there any way to color each category with a different color in cytoscape? or R? My input is 2 column ...
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1 answer
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How to build advanced boxplots from datasets which columns contain only numbers?

I have got a fold-change dataset and I simply would like to plot something like this: The problem is that I have only numbers in my columns and when I use a boxplot() function I can plot only boxes ...
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How to manage memory contraints when analyzing a large number of gene count matrices? I keep running out of RAM with my current pipeline

I have several hundred scRNA-seq count matrices, each from a different sample. For my other dataset containg a few dozen samples, I simply merged everything together into one Seurat object, but that ...
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2 answers
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"Error in col2rgb(colors, alpha = TRUE) : invalid RGB specification" when running HeatmapAnnotation() (from ComplexHeatmap)

This question was also asked on github I'm trying to run the function HeatmapAnnotation (a function in the ComplexHeatmap package). When I run it, I get the error "Error in col2rgb(colors, alpha =...
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2 votes
1 answer
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baseMean threshold

I have an RNA-seq dataset and I am using DEseq2 to find differentially expressed genes between the two groups. I used pre-filtering to remove any genes that have ...
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Missing value imputation method for gene expression data

I am new to working with gene expression data sets and am wondering what is the most standard or best way to impute missing values in a gene expression data? I got mine from the GEO database and the ...
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Subsetting with harmony

Currently merged two Seurat objects together and then ran Harmony for batch correction. Now I want to subset out a cell type of interest do I re run harmony or just do the standard PCA? ...
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2 votes
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Subsetting out prefix from genes and merging

I'm working with PTX samples (human and mouse), they're aligned to both transcriptomes and so gene names contain hg38- and mm10- at the beginning of each gene. I have eliminated teh prefixes because I ...
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Where to find asymmetric nucleotide substitution matrix with IUPAC encodings?

I am using the pairwiseAlignment function from the Biostrings package to calculate the distance between a consensus sequence and ...
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Problem of writing scilab code on a project - Morris-Lecar model

This is a computational neuroscience project. We are asked to plot the Morris-Lescar model (question 3 below). The model should be plotted with scilab or R. however, I don't know where to start? For ...
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3 votes
0 answers
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Grouping x-axis in scatter plot

I am trying to plot one scatter plot for each group, where each group has continous values in x-axis. Reference Data Gives continuous x-axis but all groups are combined. ...
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  • 355
1 vote
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open source tools for CNV analysis from illumina SNP array

What are the best open source tools to analyse copy number variation using Illumina SNP array data...preferably R based tools, but open to other languages as well. I'm working with leukemia sample and ...
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111 views

DimPlot - How to highlight cells with identity colors?

I made this wrapper for DimPlot: ...
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0 answers
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Error loading DiffBind sample sheet

I am trying to analyse a ChIP-Seq data set with DiffBind. These are the contents of my sample sheet ("diffbind_samples.csv"): ...
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Is there a generally accepted method used to impute missing DNA methylation data (probe beta-values)?

I'm looking at DNA methylation (DNAm) data such as TCGA (e.g., BRCA, KIRP, KIRC, etc.). Currently trying to build use my model to predict DNAm age on test sets, but many of the data sets are missing ...
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2 votes
0 answers
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Pulling out genes in a scatterplot

I'm comparing gene expression among 2 different datasets (in vivo and in vitro) I have made a heatmap showing the correlation for each and then plotted the data frame to create a scatterplot. Now I ...
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LRT test in deseq2 on multiple condition

I have some doubts when i'm running LRT This is my condition data-frame small subset ...
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3 votes
1 answer
47 views

Constructing Two Triangle Heatmaps in One Square

I'm looking to make a two, two range colour scheme heatmap where each range corresponds to a separate triangle in the heatmap square. I am looking for a relevant guide for this heatmap. Any ...
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2 votes
1 answer
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Wrapping R scripts in WDL and run in docker

I am trying to run an R script as a task in WDL in a docker image. Since this is my first time working with these, I am stuck in something very simple (and in the initial stage) and am hoping somebody ...
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1 answer
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A two color bar plot in R

I have raw read counts of miRNAs in two conditions like below ...
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0 votes
2 answers
27 views

subsetting more than one ccle sample

I'm working with the CCLE dataset and I'm trying to subset the data to just 3 cell lines of interest but not sure how to it. Currently, I have been subsetting one by one but is there an easier way? <...
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-1 votes
1 answer
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Selecting a part of heatmap

I have a heatmap I see a block of genes for a group of samples How I can select a part of heatmap? I mean is there any way to export a list of genes from rows of a heatmap in R? I have tried which ...
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3 votes
2 answers
75 views

How to subset a GRanges object based on a specific genomic window of interest?

Goal: To keep only rows of a GRanges object if their start coordinate is within 1 Mb of the start coordinate of a gene of interest. I am aware of some functions that come close: ...
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3 votes
2 answers
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Plotting a gene in Seurat

I saw in the extensive Seurat documentation for Dimplot (dimensional reduction plot), here, you can plot a gene by specifying it with group.by = "gene" but this does not work in practice. <...
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0 answers
105 views

Featureplot by co-expression of some genes

I want to identify MDSCs cells which don't not express HLA-DRs (HLA-DR negative) but express ...
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2 votes
1 answer
46 views

Displaying BIC and AICs from MSA nucleotide multisequence fasta file

I am initiating a project reproducing MEGA style trees using R to find the best DNA protein models under AIC/BIC. I have read the R AICs and BIC documentation but I'm struggling to implement this. ...
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4 votes
1 answer
49 views

Co-occurrence networks in Metagenomics studies

I have recently acquired some 16S metagenomics data, and was wondering if anyone can speak of the potential limitations, challenges as well as advantages to conducting a network-based study on ...
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1 vote
0 answers
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Separation of dihedral angles of the desired sequence in the protein

have a list of pdbid and I want to separate the dihedral angles of some sequences in protein . ...
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1 vote
0 answers
13 views

Different output on same command and same input file, different library version

I am running a variant calling pipeline to detect solid tumours and haematological alterations. The variant calling is done with Mutect2, whereas I am using an R script to perform some filtering on ...
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2 votes
1 answer
157 views

In a RNA-Seq heatmap should you do Z-score standardisation before clustering the rows/columns or after?

I have made a heatmap using RPKM values from a RNA-Seq dataset using the pheatmap() function in R. I have log2-transformed the data before performing Z-score standardisation of the data. I have also ...
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  • 157
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1 answer
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How to remedy a DESeq2 collapsing technical replicates error?

Goal: To ensure "the sum of the counts for [my samples] is the same as the counts in the [samples] columns in ddsColl" after collapsing replicates using ...
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1 vote
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How can I get a column with real gene names in my ballgown analysis?

I am doing RNAseq analysis and I am using ballgown procedure for it. There is an option in R to calculate differentially expressed genes and use FPKM in calculating differential gene expression, which ...
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0 answers
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Should I remove days_to_death = 0 before TCGA survival analysis

Some patients in TCGA data have days_to_death = 0 and days_to_follow_up = NA vice versa. Should I remove these samples before survival analysis? What does days_to_death = 0 mean? Does it mean the ...
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0 votes
0 answers
33 views

Combine different FASTQ belonging to different hypervariable 16s regions

I'm really newbie in 16s microbiome analyses, so sorry for this question. I would like to perform a meta-analysis using only Illumina Amplicons sequences from different studies that have different ...
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  • 101
1 vote
1 answer
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RNA-Seq Data Heatmap: Is it necessary to do a log2 transformation of RPKM values before doing the Z-score standardisation?

I am making a heatmap using RNA-Seq data in R. The heatmap shows gene expression values (RPKM) in different brain regions. I have the following code: ...
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0 votes
0 answers
27 views

install a CRAN package that imports a CRAN package that imports a Bioconductor package

I have a CRAN package say myPack, that imports two CRAN packages, say cranA and cranB. These ...
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0 votes
2 answers
27 views

How Does Cox Proportional Hazard Model Describe Interaction between Covariates

I have read STDHA and the documentation for the coxph() function in R. I understand that the cox PH model explores how different covariates simultaneously impact survival. Based on the Lung data ...
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1 vote
1 answer
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Best methods for clustering heatmap based on regions where the genes are most highly expressed?

I am analysing RNA-Seq data for a set of genes from different human brain regions using data from the Allen Brain Atlas. I have made a heatmap using GraphPad Prism. In this heatmap, I show the average ...
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0 votes
0 answers
116 views

Calculate allele frequency from VCF file in R package

I have performed variant calling using the Platypus tool but cannot find allele frequency (AF) in the output file. I am trying to read the vcf file in ...
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0 answers
30 views

Error in step 2 of SAIGE anlayses

Has anyone used SAIGE for analyses? I get the following error at step 2. I have also asked this question on GitHub. ...
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1 vote
2 answers
69 views

Reading in external single cell data

I'm trying to read in an external single cell dataset from https://www.nature.com/articles/s41467-020-16164-1, but I am having trouble reading in the count matrix. counts found here: https://www.ncbi....
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  • 317
1 vote
1 answer
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maxEE parameter from DADA2 package in R

I have just started the QC steps from the dada2 pipeline, and have failed to find a detailed explanation of what the maxEE argument entails. I have surfed many forums, as well as the details given by ...
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0 votes
1 answer
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Calculating dn/ds ratio between two model organisms

I am trying to calculate the dn/ds ratio between the human genes and c.elegans. However, I am getting NA values in the output file I used the following script ...
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0 votes
0 answers
37 views

Error generating count data using featurecounts in R

I am doing some RNA analysis and am having issues trying to generate count data. I mapped my reads to a reference genome fasta file (genbank fasta file from ncbi) using bbmap and .sam files as the ...
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2 votes
0 answers
28 views

How to identify in a RNA seq data in which sample is in which cell using R using qusage

I am using RNA seq data and have been using QuSage in R in hopes to try to identify different samples and figure out which cell it belongs to. I am trying to visualize and utilize the results but I am ...
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1 vote
1 answer
309 views

Changing the order of colors in pheatmap

I plotted a heatmap I want cancer to be red and healthy to be blue ...
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1 vote
0 answers
37 views

How to split genotypes into two groups from a SNP txt file contains -1, 0 and 1 in R?

I have a SNP file(it is 96 obs. of 1178 variables with -1, 1 and 0 and in some places NA) and I need to calculate Jaccard genetic distance from them in R. Is there any way to convert these 3 values to ...
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