Questions tagged [r]

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5 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. ...
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25 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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2answers
47 views

Changing the name of elements in a column

I have a very big matrix like ...
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1answer
30 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 ...
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1answer
24 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 ...
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2answers
59 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 ...
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1answer
12 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 ...
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1answer
42 views

Putting cells in Seurat dimplot selectively

I am going to adjust Seurat dimplot in a way avoiding some cells so both my dimplot and heatmap look nice If you please consider this picture, you would see some cells are far from the clusters so I ...
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2answers
33 views

Uploading files from local computer or web in rstudio cloud

I am using RStudio Cloud for running velocyto R package. So I have tried to import velocyto file from http://pklab.med.harvard.edu/velocyto/mouseBM/SCG71.loom I tried to upload that like so But ...
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1answer
29 views

Seurat VlnPlot presenting expression of multiple genes in a single cluster

Seurat VlnPlots are most commonly used to visualize differences in any given gene expression across multiple clusters or cell types. For example: ...
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1answer
46 views

Binding columns with matched elements

I have a matrix in which sample IDs are in rows and genes are in column like below ...
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2answers
36 views

Trim Seurat object to contain expression info only for selected genes

I'm working with some large Seurat objects (MOCA, MCA, Tabula Muris) studying gene coexpression, and I'm running into memory issues. Is it possible to remove all genes in a Seurat object that are ...
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0answers
28 views

How to set equal distances between axes ticks irrespective of number of points I plot in a ggplot?

how can I set an equal distance between the ticks of axes in a ggplot irrespective of the number of items I plot? For example I want to have the kind of plot below from Seurat's ...
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1answer
68 views

How I move these files based on their names in R or terminal

EDITED I have list of my samples in first column and corresponding file name for my .vcf files in second column of a file name clin_name.txt like below. For ...
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1answer
12 views

WGCNA module preservation error code with plotting summary statistics

I am trying module preservation with WGCNA using my own data. I am plotting the summary statistics including Zsummary, medianRank, observed IGP and IGP permutation p-value for two comparison data sets....
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2answers
174 views

How to loop multiple function in shell script?

I need to extract sequences one after another consecutively from a large fasta files (multiple fasta files) and each extracted files to be saved in new fasta file (I mean the first sequence extracted ...
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0answers
21 views

Should I use log2-CPM values (voom-limma) as input for my model?

We have created a model to integrate several OMICs data, but we realized that the maximum TPM values of RNA-Seq data were so big that had unexpected effects on our results. We hypothesized that this ...
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4answers
100 views

How I can change the name of multiple files at once in R or terminal?

I have 200 .vcf files in a folder with long names like LP6005409-DNA_E03_vs_LP6005408-DNA_E03.snp.pass.vcf How can I change the name of each file to, for ...
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2answers
16 views

How can I find all the columns available in UniProt.ws package for R?

I am trying to find the subcellular localization of my 10,000 proteins using UniProt.ws package for R. However, I am unable to find all the columns available for query. I used another package named ...
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2answers
17 views

HVG and variation coefficient

I'm looking for highly variable genes from a data set. I have calculated the coefficient of variation of the expressed genes of my dataset and inserted them in a histogram graph. Now I should select ...
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2answers
49 views

GenomicRanges: get nearest neighbor distances for random genes using a for loop

I want to compute the nearest neighbour distances using a for loop. I can do this with a random subset by doing this: ...
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1answer
168 views

How I loop over this code

I have 139 samples; In R for each sample I run below codes for example for sample 1 ...
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1answer
26 views

Replacing some strings in R or terminal

I have a .txt file; I have 139 unique sample IDs in sampleID column ...
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0answers
33 views

How to interpret Mendelian randomization results?

I did Mendelian randomization using this software: https://cran.r-project.org/web/packages/MendelianRandomization/vignettes/Vignette_MR.pdf ...
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1answer
48 views

Pattern mining from a genomic sequence

I need to find the following pattern from a genomic sequence ...
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1answer
21 views

Customizing colors in geom_arc_bar (ggforce)

I am trying to plot scatter plot of pie charts using ggplot2 and ggforce. Following is my code ...
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1answer
37 views

Parsing MSigDB Supplementary Collections

MSigDB recently added Supplementary Collections. The formatting is similar to the original MSigDB gene sets, but there is an additional metadata.txt file (link). ...
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0answers
18 views

Calculating True Positive Rate with qvalue function

I was wondering if there is something I am doing wrong when trying to calculate True positive rate, TPR with your function this is what I am doing: ...
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0answers
7 views

WGCNA R correction for different sample sizes in module trait comparison

I am doing WGCNA analysis and relating modules to external traits. Within my sample I have 51 samples in one trait or interest, 49 in another trait of interest and 48 in the 3rd trait of interest. I ...
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1answer
22 views

WGCNA module preservation

I am completing the online tutorials for module preservation of human brain modules in chimpanzee brains and vice versa (III). If anyone is aware of this tutorial or practiced before wondering if can ...
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1answer
47 views

How I deal with this expression set?

I have a gene expression raw counts like below for 16 patients ...
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1answer
30 views

Tree cut issue in WGCNA

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1answer
39 views

correlation between transposon and gene

I have two matrix identical in N° of rows and columns. In the first matrix rows indicate transposable elements and columns indicate samples. the matrix show the degree of expression of each element ...
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3answers
83 views

Which correlation method to compute the correlation score between different clusters of Sc-RNAseq data?

I'm analyzing single cell rna-seq data and trying to compute the correlation score between different clusters. Wondering how to choose the correlation method("pearson" (default), "kendall", or "...
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1answer
101 views

Doing plot with this data

I have normalized expression values of some genes in some patients and the how many days they have survived from their diagnosis with cancer like below EDITED I have taken mean of the expression ...
2
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2answers
59 views

How I swap rownames in these data?

I have a microarray gene expression matrix like this by weird gene IDs in rows. > head(mat[1:10,1:5]) > dim(mat) [1] 39302 76 > There is matched ...
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2answers
32 views

How to retrieve values from one table that corresponds to the values in another table in R

I have following table. structure(list(n = c(29L, 11L, 10L, 10L), domain = c(1L, 5L, 6L, 32L)), row.names = c(NA, -4L), class = c("tbl_df", "tbl", "data.frame")) ...
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2answers
29 views

R WGCNA error code

I am using WGCNA to identify Consensus modules. I get a warning message when completing the following step: Call the network topology analysis function for each set in turn Warning: ...
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1answer
47 views

Investigate the effect of street-light regime on insects

I need advice on a suitable analysis of a dataset that has an awkward design - because we investigate a real-world situation -we have two sites (A,B) where we can conduct the research. The hypothesis ...
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0answers
38 views

Row labelling in a heatmap in R

Could I have specific row labels in bold text but not all of them when creating a heatmap using R? (eg. using heatmap.2 function)
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1answer
17 views

How to map selected genes to Metabolic pathway Maps

I have a selected Arabidopsis Genome Initiative (AGI) list for RNA seq and proteomics data, how can I map them to metabolic pathway maps to vilualize(e.g. TCA cycle / FA / Photosynthesis) in KEGG or ...
2
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1answer
71 views

How to load and split my two individual datasets when integrating datasets in Seurat?

I want to do comparative analyses of my two individual single cell RNA-Seq datasets in Seurat. And I load and list my data as follows: ...
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0answers
53 views

Create a Heatmap that uses modules of genes rather than individual genes in Seurat

Is it possible to create a Heatmap in Seurat that takes in and displays modules of genes as its features rather than individual genes? So if I have a module of genes associated with a trait or ...
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0answers
36 views

module differential connectivity (MDC) analysis

Paper in this paper I am citing the lines below . ) Intra-modular connectivity of resilient and susceptible network modules was compared to that of corresponding genes in control mice to identify ...
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1answer
114 views

Changing the axis limits of ggplot objects

By EnhancedVolcano R package I have this plot with this code ...
0
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1answer
81 views

How I deal with this kind of gene expression comparision

I have RNA-seq from two sequencing batches; Lab technician says that he has run the RNA expression quantification two times in bathes 1 and 2 for example tumor 1 in batch 1 and tumor 1 in batch 2 , ...
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0answers
41 views

Module preservation analysis WGCNA

I have done a WGCNA (weighted gene co-expression network analysis) analysis for various brain disorders. So along with control, I have 3 different disorders such as BPD, MDD and SCZ. Now I have to ...
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2answers
89 views

Interpreting this PCA plot for RNA-seq

I have RNA-seq from two sequencing batches; Lab technician says that he has run the RNA expression quantification two times in bathes 1 and 2 for example ...
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0answers
43 views

Want to make a tsne plot show subset

I am new to R. I make a tsne plot for my data "yfp". And there are two subsets in my data (yfppt and yfpng). I want to show their distribution or location in yfp tsne plot but failed. And I even did ...
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0answers
33 views

How to run function “convolve” in parallel in R?

I have a vector of 200 million numbers. It has been running for over 24 hours and still not done. ...