# 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.

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39 views

### Joining columns to a sorted file

I have had a segmentation file (copy number) like below ...
28 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 ...
37 views

### What does this statement mean?

I have a copy number segment file with this by SCAT R package ...
41 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 ...
12 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 ...
55 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 ...
48 views

### How I remove variants ovelapping common genomic ranges? [closed]

I have a copy number file like ...
30 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 ...
58 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 ...
35 views

### Griding ggplot object in r

I have this data frame head(d) ...
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 ...
65 views

### Showing name of genes in boxplot

I have a long format data frame like this ...
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 ...
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 ...
174 views

### How to add an increment to a repeated strings

This is my data dput(METADATA) ...
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 ...
79 views

### Converting values to string

I have a data frame ...
45 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 ...
59 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 ...
81 views

### Making a volcano plot look less cluttered

I have generated a volcano plot with a differential expression file. Code for inputing file: ...
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) ...
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) ...
94 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: ...
36 views

### Calculating mean accross rows with repeated entries in R

I have this expression matrix ...
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 ...
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 ...
44 views

### Chaning string in rows

I have a too big data frame ...
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 ...
36 views

### Merging two data frames

I have a data frame like with more samples like ...
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 ...
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....
27 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: ...
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
36 views

### Appending some columns from one tabular file to another

I have a list of files in which I have this information ...
24 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 ...
50 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 ...
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 ...
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 ...
59 views

### Replace a prefix of a string

I have a data frame like this ...
47 views

### Making some columns if a dataframe numeric

I have two dataframes ...
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 ...
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 ...
47 views

### Merging matched parts of two dataframes

I have a big data frame like this ...
24 views

### Adding new columns to this data frame

I have a dataframe like this ...
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 ...
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 ...
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 ...
76 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 ...