R package to analyze data after small RNAseq with bcbio
Home Page: https://lpantano.github.io/bcbioSmallRna/
License: MIT License
Quality control and differential expression for bcbio small RNA-seq experiments.
This is an R package.
BiocManager("lpantano/bcbioSmallRna")install.packages("devtools")
devtools::install_github("lpantano/bcbioSmallRna")
Trying to load a bcbio run with these commands:
path <- "/home/kokyriakidis/Downloads/BCBIO/mirqc_bcbio/final/2020-02-23_mirqc_bcbio"
sbcb <- loadSmallRnaRun(path, "condition")
And I get:
Error in x[[...]] <- m : replacement has length zero
3.
`[[<-.factor`(`*tmp*`, "sample", value = NULL)
2.
`[[<-`(`*tmp*`, "sample", value = NULL)
1.
loadSmallRnaRun(file.path(path, "final", "2020-02-23_mirqc_bcbio"), "condition")
I did some digging in the code. First, this change is necessary I think.
match <- str_match(project_dir, project_dir_pattern)
should change to:
match <- str_match(basename(project_dir), project_dir_pattern)
The part that breaks the code is this:
csv <- read.csv(csv_file, row.names = 1L, check.names = FALSE)
#This line breaks the code# csv <- csv[, apply(!is.na(csv), 2, all)]
if (is.null(colData)) {
col_data <- csv
}
else {
col_data <- as.data.frame(colData)
}
col_data[["sample"]] <- rownames(col_data)
Removing this line makes the function work fine. This is happening when there is only one column with info about the samples and after the removal of the other fields, the format is disrupted.
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