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.

Filter by
Sorted by
Tagged with
-2
votes
0answers
25 views

How to install UnThermo R package?

There is this R package that apparently can be used to convert Thermo Fisher RAW instrument files. But there is no description provided on how to install it. Does anyone know how to install it? https:...
1
vote
1answer
30 views

DoHeatmap Hierarchical Clustering Seurat

I have a list of genes that I'd like to visualize using the DoHeatmap function in Seurat. However, the output of the heatmap does not result in hierarchical clustering and therefore makes it very ...
2
votes
1answer
38 views

Using `install.packages` with conda-managed R

I have R installed and managed by conda (miniconda) on my MacBook Pro. The version of R I use most frequently (3.5.1) is installed on the base environment and I have other version-specific ...
0
votes
1answer
40 views

Trying to change the element of a specific coordinate in a dataframe in r

So I am analyzing RNA sequence data, and putting my data into an excel spreadsheet. The way I am doing that is taking lists, and converting them to data frames, that I then cbind.data.frame together ...
-1
votes
1answer
36 views

R error: could not find function “pathwayAnalysis”

...
0
votes
1answer
52 views

Why is 42 the seed used in RunPCA() in Seurat?

The RunPCA() in Seurat 3.0 function has seed.use=42 by default. How does one choose a seed number? Is this chosen simply because ...
0
votes
1answer
19 views

Error: package or namespace load failed for 'ChIPseeker'

How do I solve the problem of loading the bioconductor Chipseeker package? I have installed in the following way and I having an error while loading it and I do not know why. ...
1
vote
0answers
27 views

How can I correctly get 3D scatter plot for micro-array pheno data in R [updated]?

I intend to see data points distribution (each reows) within labeled groups (different batchs such as 1,2,3, and so on) in 3D scatter plot, because I want to see the distribution of the data points ...
0
votes
1answer
35 views

Reducing a string to a certain amount of the first characters in R

So I have a list of several thousand RNA transcripts, and I am trying to find out how they are spliced. Right now I am running matchLRpatterns() from the Biostrings ...
0
votes
0answers
24 views

Create samples of cells for the limma package

I have an aggregated sample that consist of yellow and non-yellow labeled cells. The objective is to find differentially expressed genes between these two groups of cells using the limma package. How ...
0
votes
0answers
26 views

How to find essential genes by differential expression from TCGA 3rd level CNV data?

I have two types of data one have normal patients copy number variation (CNV) data and another have tumor patients CNV data. In each file there are three columns one contain patient ID, second ...
0
votes
2answers
59 views

Run Rscript for multiple samples (files)

I have used the following script for calculating the median for one file (gene). However, I have 20,000 files for which I want to run this R script and get 200 separate output files ...
0
votes
0answers
41 views

Any way to filter out highly correlated genes with limma linear model?

I have Affymetrix gene level expression matrix (genes in the rows and sample ID on the columns), and I have annotation data of microarray experiment observation where sample ID in the rows and ...
0
votes
0answers
12 views

How to order grouped elements in Gviz

Gviz is useful for visualization of gene transcripts by genomic coordinates. I'm using it to show the difference between splice variant transcripts. However, it seems that the ordering of transcript ...
1
vote
1answer
22 views

Any way to quantify the variation of genes that expressed in Affymetrix expression data?

am experimenting preprocessed Affymetrix microarrays expression data matrix (Affymetrix probe-sets in rows (32830 probesets), and RNA samples in columns (735 samples)) for my downstream analysis. Here ...
0
votes
3answers
92 views

Import gene list to Seurat to define cell types

Is there a way to import gene list into Seurat to define cell type? The default cell types in Seurat is not enough for our research. For example, we want to mark a subtype of B cells in Seurat, but ...
4
votes
1answer
92 views

Find intervals that genes fall within their range

I am trying to run some frequency based stats to identify selective sweep in my study system using Rpackage "PopGenome". To proceed with it I have split my genome data (whole genome sequencing) into ...
3
votes
2answers
78 views

Issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?

I would like to visualize tree with multiple sequence alignment. My din.newick file is shown below, ...
1
vote
1answer
38 views

Error Code in WGCNA: Dealing with large data sets: block-wise network construction andmodule detection

I am comparing single block module detection with 2 block module detection in WGCNA. Does anyone know what this relates to? I have rechecked and rechecked my codes for both the single and 2 module ...
0
votes
1answer
26 views

Why does DESeq2 convert numeric columns to factor during differential expression analysis?

I'm attempting to perform differential expression analysis using DESeq2 on a dataset of ~90 samples and ~20000 transcripts. I have a number of variables I'd like to test against, some of which are ...
1
vote
2answers
27 views

Getting a stretch of genomic ranges from a dataframe/granges object based on metadata column

I have a "test" data.frame object in R, which is basically a small subset of a 66000 row dataframe, which looks as follows: ...
0
votes
0answers
44 views

Normalization of data with rpkm

I'm very i difficult with normalization of my data. I was searching for transposable elements in my genome, and after this step, I made counts of reads in some transcripts. I produced something like ...
0
votes
1answer
43 views

how can i download rna-seq data sample for starting rna-seq analysis by R? [closed]

I am looking for an induction into RNA-seq analysis using R. I have yet to decide a data set, or a subject area. Any help in this regard would be welcome.
1
vote
1answer
56 views

Kruskal–Wallis and wilcox.test choice of test for expression data

I have bit of confusion regarding how ggpubr has implemented the KW and wilcox.test. By default usage of ggpubr reports p value for wilcox.test() but when it comes to Kruskal–Walis it is different . ...
-1
votes
1answer
50 views

How I normalize these two sets of data

I have average log fold change for a cluster of cells versus another cluster of cells by Seurat like below ...
2
votes
1answer
49 views

Protein SCA and DCA

Could you please suggest suitable R packages for statistical coupling and direct coupling analysis of protein sequences? I know there are Python packages for those: SCA and DCA. I was looking for ...
0
votes
0answers
37 views

Easy filtering seurat metadata based on knn results

Given a Seurat object I'm trying to get the metadata of neighbors cells (knn) to a given cell. I'm trying to create some score for each cell based on its snn neighbors. The score is: ...
1
vote
1answer
80 views

Align legends to each heatmap in a ComplexHeatmap with 2 heatmaps

I have created a ComplexHeatmap containing 2 Heatmaps, each with their own legend. The legend on the first Heatmap is continuous, whereas that of the second is ...
2
votes
1answer
133 views

How do I add a colour annotation bar to the heatmap generated by DoHeatmap function of Seurat v2?

I am using Seurat v2 for professional reasons (I am aware of the availablity of Seurat v3). I am clustering and analysing single cell RNA seq data. How do I add a coloured annotation bar to the ...
0
votes
2answers
57 views

Reading a txt in R with weird header

I am trying to read a txt file in R but always I am getting ...
-4
votes
1answer
82 views

Finding matched genes for each genomic range

I have called structural variants and now I have ...
1
vote
1answer
93 views

WGCNA error codes in Network Construction & moduel detection

I am using WGCNA and code has worked with no problems with some of my datasets however with most recent attempt when completing gene network & identification of modules. I get following error code....
0
votes
1answer
26 views

Generate table for total number of SV events per sample

I have called and annotated structural variants and I have a table by name of samples and structural events like below ...
1
vote
2answers
84 views

GSEA - Gene Set Enrichment Analysis - in R studio

I have been trying to conduct a classic GSEA using the broad institute software and can not figure out how to compile it in R for the life of me. I am aware that there exists other packages in R that ...
2
votes
0answers
30 views

How can `limma` be used to determine genes predictive of a given phenotype?

Using limma and lmFit on gene expression data, I can perform a series of regressions ...
2
votes
2answers
110 views

Interpretation of hierarchical clustering with bootstrapping

I have data that includes 'cases' and 'controls' and have carried out hierarchical clustering. I used the pvclust package in R to bootstrap the results and ...
1
vote
0answers
45 views

How to write the subclusters in file?

I have constructed a gene co-expression network from RNA-seq data. The network file is in edge list format of memory around 1gb which was created by calculating Pearson correlation of each gene pairs ...
1
vote
1answer
57 views

Voom transformation of RNA seq raw counts data

I have RNA seq data of raw gene counts that I want to transform for linear modelling. I am trying to voom transform, to do a weighted analysis. Data frame: prac_count_10 ...
1
vote
0answers
31 views

How can I convert Affymetrix microarray data to bedgraph format?

I've previously asked a different question about the ChIP-chip microarray data that I'm working on. I'm new to this so I'm sorry for asking here again. I have .CEL files and I'm using the Affy ...
-1
votes
2answers
97 views

How I debug this code?

I am trying to run CMSclassifier::classifyCMSfunction on my data but I am getting this error ...
1
vote
1answer
112 views

Clustering of gene co-expression network by igraph R package

I have constructed a gene co-expression network from RNA-seq data. The network has more than 10000 nodes and more than 1 million edges. The network file as an edge list format of memory around 1gb ...
2
votes
1answer
61 views

Pattern matching and removing from the name

...
1
vote
0answers
32 views

ExpressionSet with a custom gene list

After an ExpressionSet is established, I want it to contain only the genes of my choice ("selected.txt") What is the best approach?? Thanks
0
votes
1answer
74 views

Plot a circos plot to show the consistency between 2 samples

I have called SNP and INDEL in two matched samples by strelka and extract this information from .vcf file and I have these ...
-2
votes
1answer
74 views

Adding a string to start of one column [closed]

I have this dataframe ...
2
votes
1answer
77 views

Significant gene set testing - limma

While I have used my title, it is more of a general statistics question regarding how these significance tests are carried out, these include decideTests and ...
1
vote
1answer
54 views

Extracting expression data in r from GEO and got a S4 object

I want to open the expression data GSE9838 dataset from GEO using GEOquery R package. gset <- getGEO(filename="GSE9838_family.soft.gz") The result of this ...
1
vote
1answer
54 views

how do I convert a vcf file for a GWAS study (using R package vcfR)

I have a vcf file with individual level genetic data, that I read using the R package vcfR ...
3
votes
1answer
68 views

How to extract gene expression tables from this GEO dataset?

I've downloaded this GSE43013 dataset using GEOquery in R. My understanding is that it contains expression data from liver, kidney, and brain for multiple species. I would like to produce gene ...
0
votes
1answer
36 views

Differential expression analysis when nested effects

I have 3 tumour samples from 3 patients from an experiment, I also downloaded 10 normal samples from TCGA. My design is like this ...