lintr-bot
commented
4 years ago R/doubletDetection.R:5:1: style: Lines should not be more than 80 characters.
#' @param sampleLabels Numeric vector. Each cell will be assigned a sample number.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/doubletDetection.R:11:51: style: There should be a space between right parenthesis and an opening curly brace.
runScranDoubletScore <- function(sce, sampleLabels){
^~R/doubletDetection.R:15:8: style: Place a space before left parenthesis, except in a function call.
for(num in allSampleNumbers){
^R/doubletDetection.R:15:32: style: There should be a space between right parenthesis and an opening curly brace.
for(num in allSampleNumbers){
^~R/doubletDetection.R:17:24: style: Commas should always have a space after.
sceSub <- sce[,sceSubIx]
^R/doubletDetection.R:29:1: style: Lines should not be more than 80 characters.
#' @param sampleLabels Numeric vector. Each cell will be assigned a sample number.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/doubletDetection.R:38:47: style: There should be a space between right parenthesis and an opening curly brace.
runDoubletFinder <- function(sce, sampleLabels){
^~R/doubletDetection.R:43:8: style: Place a space before left parenthesis, except in a function call.
for(num in allSampleNumbers){
^R/doubletDetection.R:43:32: style: There should be a space between right parenthesis and an opening curly brace.
for(num in allSampleNumbers){
^~R/doubletDetection.R:46:36: style: Commas should always have a space after.
sceCountsSub <- sceCounts[,sceSubIx]
^R/doubletDetection.R:51:33: style: Put spaces around all infix operators.
normalization.method="LogNormalize", scale.factor = 10000,
~^~R/doubletDetection.R:78:31: style: Put spaces around all infix operators.
nExpPoi <- round(0.075*ncol(seurat@assays$RNA))
~^~R/doubletDetection.R:112:51: style: There should be a space between right parenthesis and an opening curly brace.
algorithm = c("doubletscore", "doubletfinder")){
^~R/doubletDetection.R:114:7: style: Place a space before left parenthesis, except in a function call.
if(is.null(sampleLabels)){
^R/doubletDetection.R:114:29: style: There should be a space between right parenthesis and an opening curly brace.
if(is.null(sampleLabels)){
^~R/doubletDetection.R:115:31: style: Commas should always have a space after.
sampleLabels <- rep(1,ncol(sce))
^R/doubletDetection.R:119:7: style: Place a space before left parenthesis, except in a function call.
if("doubletscore" %in% algorithm){
^R/doubletDetection.R:119:37: style: There should be a space between right parenthesis and an opening curly brace.
if("doubletscore" %in% algorithm){
^~R/doubletDetection.R:120:13: style: Use <-, not =, for assignment.
sce = runScranDoubletScore(sce = sce, sampleLabels = sampleLabels)
^R/doubletDetection.R:122:7: style: Place a space before left parenthesis, except in a function call.
if("doubletfinder" %in% algorithm){
^R/doubletDetection.R:122:38: style: There should be a space between right parenthesis and an opening curly brace.
if("doubletfinder" %in% algorithm){
^~R/doubletDetection.R:123:13: style: Use <-, not =, for assignment.
sce = runDoubletFinder(sce = sce, sampleLabels = sampleLabels)
^R/doubletDetection.R:127:1: style: Trailing blank lines are superfluous.
^
codecov-io
Add doublet detection algorithms (doubletCells, doubletFinder), as well as wrapper function for algorithms