read_STAR: Read STAR log files

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Read STAR log files

Description

Read STAR Log.final.out files and optionally reshape into wide format.

Usage

read_STAR(path = ".", pattern, reshape = FALSE)

Arguments

path	the path to STAR log files, the default corresponds to the working directory.
pattern	regular expression for file name matching, default .final.out
reshape	reshape percent mapping into wide format with samples in rows

Value

A tibble

Note

Reading output files requires a unique sample identifier in either the file name or parent directory

Author(s)

Chris Stubben

Examples

## Not run: 
 x <- read_STAR( pattern=".star.out$")
  reads <- c("Uniquely mapped",  "Mapped to multiple loci",
               "Mapped to too many loci", "Unmapped reads")
  y <- filter(x, stat %in% reads) %>% mutate( stat= factor(stat, levels=reads ))
         hchart(y, "bar", x=sample ,  y=value, group=stat ) %>%
            hc_plotOptions(bar = list(stacking = "normal")) %>%
             hc_colors( c('#437bb1', '#7cb5ec', '#f7a35c', '#b1084c') ) %>%
               hc_yAxis(reversedStacks = FALSE)
 read_STAR( pattern=".star.out$", reshape=TRUE)

## End(Not run)

HuntsmanCancerInstitute/hciR documentation built on March 26, 2024, 3:09 a.m.