How to subset s4 object
WebFeb 6, 2024 · an MAF object generated by read.maf. tsb: subset by these samples (Tumor Sample Barcodes) genes: subset by these genes. query: query string. e.g, "Variant_Classification == 'Missense_Mutation'" returns only Missense variants. clinQuery: query by clinical variable. ranges: subset by ranges. data.frame with 3 column (chr, start, … WebPrevious message: [R] S4 objects with list of objects as slots: how to subset? Next message: [R] parsing arguments of a function. Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Try: c (sapply (1:2, function (i) a.class at my.list [ [i]]@my.slot)) On 4/20/06, Francois.Bastardie at ifremer.fr < Francois.Bastardie at ifremer.fr ...
How to subset s4 object
Did you know?
WebThe SummarizedExperiment class is a matrix-like container where rows represent features of interest (e.g. genes, transcripts, exons, etc...) and columns represent samples (with sample data summarized as a DataFrame ). A SummarizedExperiment object contains one or more assays, each represented by a matrix-like object of numeric or other mode. Web4.3.3 Missing and out-of-bounds indices. It’s useful to understand what happens with [[when you use an “invalid” index. The following table summarises what happens when you subset a logical vector, list, and NULL with a zero-length object (like NULL or logical()), out-of-bounds values (OOB), or a missing value (e.g. NA_integer_) with [[.Each cell shows the result of …
WebEach slot can contain a different object class and, before operating on it, should be checked using str() or class(). The @data slot is always a data.frame object and @coords is a matrix whereas @polygons is a list object with additional … WebMar 27, 2024 · In addition to returning a vector of cell names, CellSelector() can also take the selected cells and assign a new identity to them, returning a Seurat object with the identity classes already set. This is done by passing the Seurat object used to make the plot into CellSelector(), as well as an identity class. As an example, we’re going to ...
WebJun 9, 2012 · The general suggestion is to write accessor functions like getMySlot () and setMySlot () to get the information you need. You can use the @ operator to access data … WebNov 2, 2024 · Create a new object that contains subsets of the first sequence of dna with, respectively nucleotides 1 to 1, 1 to 2, 1 to 3, …, 1 to 10. Solution (, )] %>% (, :) 4.6 Working with genomes. Copy link. BSgenome packages contain whole genome sequences as distributed by ENSEMBL, NCBI and others. In this next example we will load the whole …
WebJul 9, 2024 · In your current code, what you are doing is converting the raster into a CRS object, that's why it fails in the next line. To correctly set the CRS you have to do the …
WebMar 3, 2024 · Th subset differential gene expression in scRNA-seq. fig. S6. Characterization of a CD4+ conditional Il9 knockout mouse. ... Preprocessing and dimensional reduction was performed as previously mentioned using a Seurat object after which the dimensional embeddings were imported to Monocle3 to manually create the associated celldataset … how many dollars is 485 euroshttp://adv-r.had.co.nz/S4.html high tide minehead todayWebNov 10, 2024 · Value. S4ToList: A list with an S4 class definition attribute . IsS4List: TRUE if x is a list with an S4 class definition attribute . ListToS4: An S4 object as defined by the S4 … high tide minster leasWebNotice how the scanBam() function returns a basic R object, instead of an S4 class. Representing the alignments as S4 object is done by the GenomicAlignments package; this is especially useful for access to spliced alignments from RNA sequencing data. The names of the aln list are basically the names used in the BAM specification. Here is a ... how many dollars is 81 eurosWebDescription. The RangedSummarizedExperiment class is a matrix-like container where rows represent ranges of interest (as a GRanges or GRangesList object) and columns represent samples (with sample data summarized as a DataFrame ). A RangedSummarizedExperiment contains one or more assays, each represented by a … high tide mistleyWebWe can check if an object is an S4 object through the function isS4(). > isS4(s) [1] TRUE The function setClass() returns a generator function. This generator function (usually having … high tide minnis bay kentWebS3 objects are made up of atomic vectors, arrays, and lists, so you can always pull apart an S3 object using the techniques described above and the knowledge you gain from str(). S4 objects. There are also two additional subsetting operators that are needed for S4 objects: @ (equivalent to $), and slot() (equivalent to [[). how many dollars is 90 pesos