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.
462
questions
0
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1answer
39 views
How I change a function not to need an input
There is a function does need an input as selected genomic site across genomic regions. But my genomic region bed file already is a subset of interesting site (like promoters). I want this function to ...
-4
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0answers
47 views
1
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0answers
28 views
Permanent error with maftools
I want to remove variant including in copy number changed area by maftools but I am permanently get this error
...
-3
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0answers
57 views
Converting this data frame to a heatmap
I have CPM values for response to a drug in two RNA-seq set up. I have grouped the patients to responders and non responders to this drug and I have done pathway analysis.
This is my data
...
0
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1answer
35 views
-2
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0answers
38 views
Plotting such stack bar plot in r
I have two groups, for them I have adjusted p values for some KEGG pathways like this
...
0
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1answer
63 views
0
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1answer
12 views
Error in createMAE function: non-unique values when setting 'row.names' in TCGA LIHC Data
I am working with the createMAE() function of the ELMER Bioconductor package. While executing the createMAE() function using ...
0
votes
1answer
38 views
WGCNA: Problem with selecting soft threshold
I have 25 tumor samples with counts data. Initially, I filtered out low expressed genes and then converted counts to varianceStabilizingTransformation using ...
1
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2answers
171 views
-3
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2answers
131 views
Is it possible to do this in R
I have a big clinical data file with 96 columns like age, gender, BMI, etc
I want to see which of these clinical characteristics relate to response to chemotherapy. Response to chemotherapy divides ...
-3
votes
3answers
78 views
0
votes
2answers
44 views
Clustered column chart for single cell data
I want to create a column plot for my single cell analysis that has 2 sample types, a normal and PDAC. I want to show, the percentage of different cell types per sample type.
How do I go about ...
1
vote
1answer
58 views
Visualizing the difference among three groups
I have 3 data frames for three groups of patients and in each of them I have the number of mutation types like insertion, deletion, SNP and total of mutations for each patients. In each group I have ...
0
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2answers
77 views
Making a volcano plot look less cluttered
I have generated a volcano plot with a differential expression file.
Code for inputing file:
...
0
votes
1answer
48 views
Bar plot with error bars
I am trying to plot a box plot/stacked bar graph with error bars.
output of dput(DF)
...
0
votes
1answer
27 views
Dodged bar chart
I want to create a dodged barchart with different cell cycles for each cell type within each condition.
dput(DF_count)
...
2
votes
1answer
87 views
Pulling out a certain gene in a volcano plot
I have generated a volcano plot with a differential expression file.
Code for inputing file:
...
-2
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1answer
36 views
-1
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2answers
48 views
Making a boxplot or violinplot for several dataframe with different number of samples
I have 3 data frames for treatment of 3 different drugs and in each of them I have the number of mutation types like insertion, deletion, SNP and total of mutations for each patients. In each group I ...
0
votes
3answers
68 views
Boxplot of read length distributions from multiple samples
Newbie R user here. I want to create a plot with boxplots of read length distribution on the Y-axis, and samples on the X-axis -- like this image from doi: 10.1038/srep16498
However, I'm not sure ...
-1
votes
1answer
44 views
0
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1answer
23 views
how can i calculate p value of miRNA raw reads counts using R?
working on lung cancer project and need to find out which genes are deferentially expressed and which are not. for that i a have downloaded miRNA data set from GEO id is GSE110907. And the file i got ...
-4
votes
2answers
35 views
-1
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1answer
35 views
Removing rows containing some strings
I have a big data frame
> dim(anno_maf)
[1] 449892 132
>
In chromosome column I have chr 1 to 22 and another contigs like
...
0
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0answers
78 views
Error in my RNAseq analysis
I was following the RNAseq analysis tutorial online(https://combine-australia.github.io/RNAseq-R/06-rnaseq-day1.html) but am not obtaining the same variance values for each row in the logcounts matrix....
1
vote
1answer
25 views
Most scalable pseudotime ordering algorithm
What algorithms for linear Pseudotime trajectory construction (diffusion-based) are the most scalable to large datasets?
I'm currently using Slingshot based on the recommendation in this manuscript: ...
0
votes
3answers
71 views
How I can push a function to act on my files
I have R code takes a vcf file returns a parsed .txt output.
I have 21 vcf files in a folder
I named my R code parse_vcf_alt1 function
-1
votes
1answer
36 views
Appending some columns from one tabular file to another
I have a list of files in which I have this information
...
0
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0answers
23 views
Percentage of each cluster in Seurat
I am using Seurat to analyze my single cell data. I have 2 conditions, treated and untreated. I am trying to create a stacked bar graph in order to show the differences in cell types for each ...
0
votes
1answer
41 views
Seurat define manually a cluster and find markers
I am aware of this question Manually define clusters in Seurat and determine marker genes that is similar but I couldn't make tit work for my use case.
So I have a single cell experiments and the ...
0
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0answers
38 views
Heatmap annotation with value and colour gradient
I am trying to use ComplexHeatmap to plot heatmap with annotation.
The code that I have tried
...
0
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1answer
28 views
Processed spliced and unspliced count matrices for existing scRNA-seq atlases
Before I do this myself...
Is there any compiled batch-corrected dataset of the major scRNA-seq atlases (Mouse Cell Atlas, Mouse Organogenesis Atlas, Mouse Gastrulation Atlas, Tabula Muris, Tabula ...
0
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2answers
59 views
-2
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1answer
47 views
0
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0answers
15 views
include a glimma interface in a shiny app
I am trying to code a shiny app for RNA-Seq data analysis.
I would like to include glimma interactive plots in it.
However, in my current interface, clicking the action button ...
0
votes
0answers
19 views
Geneoverlap library data input
GeneOverlap I am trying to use this library so in the default data sets it has different list of genes which are categorized as high low or medium expressed genes. So my question is can I run this one ...
1
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2answers
47 views
0
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1answer
24 views
0
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1answer
14 views
Parallelizing WGCNA k-means clustering and merging smaller clusters
WGCNA carefully takes advantage of server parallelization in several functions, and I can switch this on with:
enableWGCNAThreads(nThreads=28)
That speeds up ...
1
vote
1answer
54 views
Merging files gives memory allocation error
I have two files like
> head(a)
chr position
1 1 136962
2 1 562020
3 1 672948
> class(a)
[1] "data.frame"
>
And
...
0
votes
0answers
15 views
Filtering criteria for selecting DEGs from Monocle3 regression analysis with categorical terms
I'm testing the package Monocle3 (version 0.2.0) with the following code. The main aim of this analysis is to identify differentially expressed genes for every time ...
7
votes
1answer
75 views
Density plot, scale it to 0-1
Doubt regarding density plot what is the scale being plotted in the Y axis.Is it possible to scale it to 1?.
This is my code
...
0
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0answers
16 views
fgsea returns an empty data frame - How to solve?
I am trying to run fgsea on a vector, v, containing Pearson's correlation. The vector names contain the corresponding gene IDs. When I run the following command, I get back an empty dataframe.
...
1
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0answers
29 views
Literature mining tools and methods
"As a first step, we sought to systematically establish the complete set of genes implicated in the physiological response to SCI. We conducted a systematic analysis of the SCI literature, reviewing ...
0
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3answers
77 views
0
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1answer
60 views
how to interpret of “pvclust” dendrogram and finding height for cutting dendrogram?
I study on RNA-seq expression dataset about one cancer in TCGA. I downloaded FPKM dataset and removed batch effect by ComBat() function. Now, I used pvclust for ...
1
vote
1answer
26 views
Illustrate a 3D visualisation of the three main PCs using plot3d() package in R?
I have a dataset (view/download) here. I need to run PCA on this data set and need to illustrate a 3D visualisation of the three main PCs using plot3d() package.
I have looked for more information ...
0
votes
2answers
82 views
how to solve “dim(X) must have a positive length” at running ComBat function in R
I used ComBat() for batch effect correction in my expression data. basically, that function inputs are expression data, Batch covariate, and Model matrix for the ...
0
votes
1answer
20 views
WGCNA correcting p value for varying sample numbers in each of the trait columns
I am correcting a data frame of sample comparison using p value. However in some columns I have different sample numbers. Within the data frame I have 4 comparisons e.g B_R, R_C, B_C, C_C. They each ...
