Questions tagged [r]

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4 views

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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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

Joinning columns from different files

I have 48 files in which I have r1 ...
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0answers
35 views

Finding difference between groups

I have mutational catalogues of 4 samples like below ...
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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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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: ...
-3
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1answer
45 views

Extracting part of a csv by a list

I have a .csv file like this ...
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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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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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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

Joining columns to a sorted file

I have had a segmentation file (copy number) like below ...
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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 ...
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1answer
43 views

What does this statement mean?

I have a copy number segment file with this by SCAT R package ...
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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 ...
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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 ...
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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

Griding ggplot object in r

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

Showing name of genes in boxplot

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

How to add an increment to a repeated strings

This is my data dput(METADATA) ...
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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

Converting values to string

I have a data frame ...
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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 ...
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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 ...
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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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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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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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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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1answer
38 views

Calculating mean accross rows with repeated entries in R

I have this expression matrix ...
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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

Chaning string in rows

I have a too big data frame ...
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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

Merging two data frames

I have a data frame like with more samples like ...
-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....
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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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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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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 ...
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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 ...
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
60 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 ...

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