EmptyDrops wrapper and unfiltered data example

R/runDropletUtilsEmptyDrops.R:2:1: style: Lines should not be more than 80 characters.

#' @description distinguishes between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment.
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R/runDropletUtilsEmptyDrops.R:4:1: style: Lines should not be more than 80 characters.

#' @param lower Numeric. The lower bound on the total UMI count, at or below which all barcodes are assumed to correspond to empty droplets.
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R/runDropletUtilsEmptyDrops.R:5:1: style: Lines should not be more than 80 characters.

#' @return SingleCellExperiment object with the emptyDrops output stored in coldata: emptyDroplet_Total, emptyDroplet_LogProb, emptyDroplet_PValue, emptyDroplet_Limited, emptyDroplet_FDR.
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R/runDropletUtilsEmptyDrops.R:15:1: style: Lines should not be more than 80 characters.

      list.of.packages[!(list.of.packages %in% installed.packages()[, "Package"])]
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R/runDropletUtilsEmptyDrops.R:16:1: style: Trailing whitespace is superfluous.

    
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R/runDropletUtilsEmptyDrops.R:20:1: style: Trailing whitespace is superfluous.

    
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R/runDropletUtilsEmptyDrops.R:24:1: style: Trailing whitespace is superfluous.

    
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R/runDropletUtilsEmptyDrops.R:25:18: style: Trailing whitespace is superfluous.

    sce.matrix <- 
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R/runDropletUtilsEmptyDrops.R:27:32: style: Trailing whitespace is superfluous.

        as.matrix(assay(sce))}, 
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R/runDropletUtilsEmptyDrops.R:38:1: style: Trailing whitespace is superfluous.

    
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R/runDropletUtilsEmptyDrops.R:39:1: style: Lines should not be more than 80 characters.

    # run DropletsUtils::emptyDrops on the count matrix, store the output to the sce@CalData, and return the updated sce.
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R/runDropletUtilsEmptyDrops.R:47:1: style: Trailing whitespace is superfluous.

    
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R/runDropletUtilsEmptyDrops.R:48:12: style: Remove spaces before the left parenthesis in a function call.

    return (sce)
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R/runDropletUtilsEmptyDrops.R:54:1: style: Trailing whitespace is superfluous.

^~

R/runDropletUtilsEmptyDrops.R:56:1: style: Trailing whitespace is superfluous.

^~

R/runDropletUtilsEmptyDrops.R:58:44: style: Put spaces around all infix operators.

  sce_test <- runDropletUtilsEmptyDrops(sce=sce, lower = 10)
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R/runDropletUtilsEmptyDrops.R:59:1: style: Trailing whitespace is superfluous.

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R/runDropletUtilsEmptyDrops.R:64:29: style: There should be a space between right parenthesis and an opening curly brace.

#for (num in allNamesSamples){
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campbio / scruff

EmptyDrops wrapper and unfiltered data example #147

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