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.
478
questions
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co-localisation error code using co-loc
Can anyway advice on what the below error code relates to. I am using co-loc R package with 2 GWAS datasets. Using coloc.abf function with pvalues, MAF, sample size and case/control cohort. Thank you
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1answer
35 views
Calculating the number of probes for a given genomic range
I have a big data frame like this for copy number (exome seq)
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1
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1answer
18 views
qvalue and p.adjust functions
Between the qvalue package and the p.adjust function, which is more appropriate to use when trying to calculate the q-values of a dataset? According to the manual for the q-value package, the q-value ...
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1answer
44 views
Merging based on Chromosome coordinates
I have a simple task which seems very complicated now
Two data-frame I have One contains the Chromosome coordinates of distal enhancer elements and other one rlog values of accessibility which I want ...
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1answer
37 views
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0answers
35 views
-3
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1answer
49 views
Error in ruuning a package in R [closed]
I want to install Signature Tools Lib R package
I typed
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5
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1answer
39 views
are GSEA and other geneset enrichment analysis supposed to yield extremely different results between them?
I have recently ran in R four geneset enrichment analysis in the same database (TCGA:breast cancer) comparing two intrinsic subtypes. The methods I used were:
MIGSA, that imports mGSZ package and ...
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0answers
19 views
Does stringDB R package require to be loaded before using it? [closed]
I am working with the package STRINGdb in R and this is the piece of code which has issues:
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-3
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1answer
45 views
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1answer
42 views
How are these definitions related to differential expression?
I have two groups of patients; for each patient I have an output file (RNA-seq) contains this information
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-1
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1answer
31 views
Drawing 2 heatmaps with the same gene order
I have 2 dataframe with same genes both different data sets
like
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1
vote
3answers
74 views
K means clustering, would PCA be a better option?
I have the data below. I need to use a clustering method to classify them and into categories of "Heterozygotote, Allele 1, Allele 2 and No Call. The values in RFU1 and RFU2 are used to determine the ...
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1answer
56 views
2
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0answers
43 views
How to deal with zeros in the denominator when calculating percent enrichment?
I have a data.frame with results from a CRISPR screen.
I want to calculate the % enrichment of a variable of interest var from ...
0
votes
1answer
43 views
1
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1answer
61 views
Reading multiple raw files in Seurat
I have multiple single cell samples to analyze and I'm following the instructions in Satija Lab's website. I want to merge all the count files from all the samples at once, and associate the metadata ...
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0answers
16 views
When running ChIPQC bioconductor package after peak calling, should I use sorted BAM files or unsorted original BAM files?
I have called peaks using MACS2 and now I'm trying to run ChIPQC bioconductor package. Can someone please tell me should I use sorted BAM files or unsorted original BAM files? I have created sorted ...
0
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1answer
68 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 ...
1
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0answers
31 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
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1answer
37 views
0
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1answer
70 views
0
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1answer
17 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 ...
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1answer
56 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 ...
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2answers
177 views
-3
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3answers
200 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 respond to chemotherapy. Response to chemotherapy divides patients to ...
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3answers
80 views
0
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2answers
46 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
77 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
90 views
Making a volcano plot look less cluttered
I have generated a volcano plot with a differential expression file.
Code for inputing file:
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0
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1answer
50 views
Bar plot with error bars
I am trying to plot a box plot/stacked bar graph with error bars.
output of dput(DF)
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0
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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)
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2
votes
1answer
140 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:
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-2
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1answer
38 views
-1
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2answers
53 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 ...
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3answers
69 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 ...
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1answer
44 views
0
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1answer
29 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 ...
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2answers
37 views
-1
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1answer
36 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
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0answers
79 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
28 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: ...
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3answers
73 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
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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
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0
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1answer
38 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
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1answer
75 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 ...
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0answers
44 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
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0
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1answer
31 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 ...
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2answers
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-2
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1answer
47 views
