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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1answer
39 views

Joining columns to a sorted file

I have had a segmentation file (copy number) like below ...
2
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0answers
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 ...
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1answer
37 views

What does this statement mean?

I have a copy number segment file with this by SCAT R package ...
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1answer
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 ...
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0answers
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 ...
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1answer
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 ...
-4
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0answers
48 views

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

I have a copy number file like ...
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0answers
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 ...
-3
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0answers
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 ...
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1answer
35 views

Griding ggplot object in r

I have this data frame head(d) ...
-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 ...
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1answer
65 views

Showing name of genes in boxplot

I have a long format data frame like this ...
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
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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 ...
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2answers
174 views

How to add an increment to a repeated strings

This is my data dput(METADATA) ...
-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
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3answers
79 views

Converting values to string

I have a data frame ...
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2answers
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 ...
1
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1answer
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 ...
0
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2answers
81 views

Making a volcano plot look less cluttered

I have generated a volcano plot with a differential expression file. Code for inputing file: ...
0
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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
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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) ...
2
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1answer
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: ...
-2
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1answer
36 views

Calculating mean accross rows with repeated entries in R

I have this expression matrix ...
-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
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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
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1answer
44 views

Chaning string in rows

I have a too big data frame ...
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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 ...
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2answers
36 views

Merging two data frames

I have a data frame like with more samples like ...
-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 ...
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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
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1answer
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: ...
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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
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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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0answers
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 ...
0
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1answer
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 ...
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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 ...
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2answers
59 views

Replace a prefix of a string

I have a data frame like this ...
-2
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1answer
47 views

Making some columns if a dataframe numeric

I have two dataframes ...
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
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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

Merging matched parts of two dataframes

I have a big data frame like this ...
0
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1answer
24 views

Adding new columns to this data frame

I have a dataframe like this ...
0
votes
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
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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
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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
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1answer
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 ...
0
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0answers
17 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 ...

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