=========================================================== .___ __ __ _________________ __ __ __| _/|__|/ |_ / ___\_` __ \__ \ | | \/ __ | | \\_ __\ / /_/ > | \// __ \| | / /_/ | | || | \___ /|__| (____ /____/\____ | |__||__| /_____/ \/ \/ grep rough audit - static analysis tool v2.8 written by @Wireghoul =================================[justanotherhacker.com]=== r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd-373-keeping track of appropriate matrices and calculating these r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd:374:offsets. For *edgeR* you need to assign a matrix to `y$offset`, but r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd-375-the function *DESeqDataSetFromTximport* takes care of creation of the ############################################## r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd-379-`countsFromAbundance="lengthScaledTPM"` or `"scaledTPM"`, and then to r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd:380:use the gene-level count matrix `txi$counts` directly as you would a regular r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd-381-count matrix with these software. Let's call this method ############################################## r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd-387-happens in 3' tagged RNA-seq data (see section below). r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd:388:The original gene-level counts are in `txi$counts` when `tximport` was run with r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd-389-`countsFromAbundance="no"`. This is simply passing the summed ############################################## r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd-405-full-transcript-length pipeline, we recommend to use the r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd:406:original counts, e.g. `txi$counts` as a counts matrix, e.g. providing r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd-407-to *DESeqDataSetFromMatrix* or to the *edgeR* or *limma* functions ############################################## r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd-465-The user should make sure the rownames of `sampleTable` align with the r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd:466:colnames of `txi$counts`, if there are colnames. The best practice is r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd-467-to read `sampleTable` from a CSV file, and to construct `files` from a ############################################## r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd-484-Because limma-voom does not use the offset matrix stored in r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd:485:`y$offset`, we recommend using the scaled counts generated from r-bioc-tximport-1.18.0+dfsg/inst/doc/tximport.Rmd-486-abundances, either `"scaledTPM"` or `"lengthScaledTPM"`: ############################################## r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd-373-keeping track of appropriate matrices and calculating these r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd:374:offsets. For *edgeR* you need to assign a matrix to `y$offset`, but r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd-375-the function *DESeqDataSetFromTximport* takes care of creation of the ############################################## r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd-379-`countsFromAbundance="lengthScaledTPM"` or `"scaledTPM"`, and then to r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd:380:use the gene-level count matrix `txi$counts` directly as you would a regular r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd-381-count matrix with these software. Let's call this method ############################################## r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd-387-happens in 3' tagged RNA-seq data (see section below). r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd:388:The original gene-level counts are in `txi$counts` when `tximport` was run with r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd-389-`countsFromAbundance="no"`. This is simply passing the summed ############################################## r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd-405-full-transcript-length pipeline, we recommend to use the r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd:406:original counts, e.g. `txi$counts` as a counts matrix, e.g. providing r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd-407-to *DESeqDataSetFromMatrix* or to the *edgeR* or *limma* functions ############################################## r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd-465-The user should make sure the rownames of `sampleTable` align with the r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd:466:colnames of `txi$counts`, if there are colnames. The best practice is r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd-467-to read `sampleTable` from a CSV file, and to construct `files` from a ############################################## r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd-484-Because limma-voom does not use the offset matrix stored in r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd:485:`y$offset`, we recommend using the scaled counts generated from r-bioc-tximport-1.18.0+dfsg/vignettes/tximport.Rmd-486-abundances, either `"scaledTPM"` or `"lengthScaledTPM"`: