search

campbio / scruff

Single Cell RNA-seq UMI Filtering Facilitator
http://bioconductor.org/packages/scruff/
Other
8 stars 9 forks source link

remove isSpike calls #173

Closed zhewa closed 3 years ago

lintr-bot commented 3 years ago

data-raw/10x/cbWhitelist737KAugust2016.R:5:1: style: Trailing blank lines are superfluous.

​
^

data-raw/exampleFastqs.R:16:1: style: Lines should not be more than 80 characters.

​ShortRead::writeFastq(v1r1fastq[seq(500)], "vandenBrink_1h1_L001_R1_001.fastq.gz")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

data-raw/exampleFastqs.R:17:1: style: Lines should not be more than 80 characters.

​ShortRead::writeFastq(v1r2fastq[seq(500)], "vandenBrink_1h1_L001_R2_001.fastq.gz")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

data-raw/Mus_musculus/barcodeExample.R:3:64: style: Commas should always have a space after.

​    "data-raw/Mus_musculus/GSE85755_CEL-Seq_barcodes_96.txt")[,2])
                                                               ^

data-raw/Mus_musculus/barcodeExample.R:6:1: style: Trailing blank lines are superfluous.

​
^

vignettes/scruff.Rmd:184:5: style: Use <-, not =, for assignment.

​sce = countUMI(al,
    ^

vignettes/scruff.Rmd:225:42: style: Commas should always have a space after.

​g <- ggbio::tracks(g1, g2, heights = c(4,1), xlab = "chr MT")
                                         ^
codecov-io commented 3 years ago

Codecov Report

Merging #173 into master will not change coverage. The diff coverage is 0.00%.

Impacted file tree graph

@@          Coverage Diff           @@
##           master    #173   +/-   ##
======================================
  Coverage    0.00%   0.00%           
======================================
  Files           9       9           
  Lines        1764    1763    -1     
======================================
+ Misses       1764    1763    -1
Impacted Files Coverage Δ
R/countUMI.R 0.00% <0.00%> (ø)
R/demultiplex.R 0.00% <ø> (ø)
R/tenxBamqc.R 0.00% <ø> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 09ac176...6fdc5be. Read the comment docs.