User: mk

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mk20
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Posts by mk

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(Closed) typeset roxygen math (\eqn and \deqn content) in html output
... I use \deqn and \eqn to typeset math in roxygen function documentation. Compiling the pdf manual produces the typesetting that I want, however, I cant find a way to compile the math and embed graphics in the html pages when I run devtools::document(). Is there any known way of doing this? ...
R roxygen latex written 24 days ago by mk20
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specify a root in igraph minimum-spanning-tree
... I have a weighted adjacency matrix and I need to create a directed MST. The problem is that I know the edge weights and the root, so I can generate an MST on an undirected graph, but I cant find a way to then specify a root. If I could specify a root, this would automatically induce directions on ...
R minimum-spanning-tree directed-graph igraph written 8 weeks ago by mk20 • updated 6 weeks ago by Biostar ♦♦ 20
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How to reproduce MATLAB tsne('algorithm', 'exact') result in R?
... Given: 1. a 25x25 matrix of integers 2. an initial 25x3 embedding, generated by PCA 3. perplexity 2 4. random seed set to 1 5. target embedding dimension 3 Run exact t-SNE using MATLAB tsne('algorithm', 'exact') and R Rtsne(theta = 0) Here is the data "A": 0 0 0 0 0 97 0 0 0 0 0 0 0 93 ...
tsne pca matlab R rtsne written 11 weeks ago by mk20
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Mapping Ensembl Gene IDs with dot suffix
... I have a bunch of bulk mRNA sequencing pulled off of the TCGA. Feature names appear to be Ensembl gene IDs with a suffix. Here is an example: > [995] "ENSG00000236246.1" "ENSG00000281088.1" [997] "ENSG00000254526.1" "ENSG00000223575.2" [999] "ENSG00000201444.1" "ENSG00000232573.1" I ...
gene ensembl biomart bioconductor written 8 months ago by mk20 • updated 6 months ago by PavolG0
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kmeans error when running reduceDimension(reduction_method = 'DDRTree')
... After setting my ordering filter, I run: > colonTumor <- reduceDimension(colonTumor, max_components = 3, > norm_method = c("none"), reduction_method = 'DDRTree', verbose=TRUE) Then I get the following error: > Error in kmeans(t(Z), K, centers = centers) : initial centers are not > ...
irlba monocle kmeans ddrtree written 9 months ago by mk20 • updated 9 months ago by Kevin Blighe31k
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Answer: A: Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assa
... turned out that fd was prepared based on a bad matrix. Issue resolved! ...
written 9 months ago by mk20
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Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assayData
... As directed in the [Monocle 2 Documentation][1], the cellDataSet constructor is called on a sparse matrix and two AnnotatedDataFrames. Here is the suggested usage: pd <- new("AnnotatedDataFrame", data = sample_sheet) fd <- new("AnnotatedDataFrame", data = gene_annotation) cds < ...
celldataset monocle expressionset written 9 months ago by mk20
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Processor count for cores with Intel hyper-threading in differentialGeneTest()
... The documentation for Monocle 2 discusses the use of multiple cores for differential gene expression. Will I be able to use each virtual core on a hyper-threaded processor? For instance, if I had an 8-core Xeon W, would I be able to make the following call: differentialGeneTest(, cores=14) D ...
hpc monocle hyperthreading rna-seq written 10 months ago by mk20 • updated 10 months ago by himanshuarya91620
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Given two sets of nucleotide n-mers, how can I learn sets of 'motifs' which are present in one and not the other?
... I have some unpublished data on DNA methylation, suggesting that there are differences in maintenance methylation efficiency at different sites from one cell cycle to another. I have a very coarse-grained approach for dividing the methylated sites into "likes to be methylated" and "really likes to ...
sequencing tf dna-methylation written 11 months ago by mk20
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Comment: C: Linking patient survival to gene-set analysis
... Thanks Kevin, removing the transcript suffix allowed me to map them to Entrez IDs as Ensembl genes. ...
written 11 months ago by mk20

Latest awards to mk

Scholar 9 months ago, created an answer that has been accepted. For A: Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assa

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