In LTLA/scRNAseq: Collection of Public Single-Cell RNA-Seq Datasets

library(BiocStyle)
knitr::opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE)

Obtaining the old version

Looks like we made a mistake in the phase assignments:the names should be G2 not G2M.

tmp <- "update_20240425"
unlink(tmp, recursive=TRUE) # get rid of any previous directory.
gypsum::cloneVersion("scRNAseq", "leng-esc-2015", "2024-04-18", destination=tmp)

Now we go in and edit the column annotations:

colpath <- file.path(tmp, "column_data")
df <- alabaster.base::readObject(colpath)

phase <- sub("_Exp.*", "", rownames(df))
phase[!phase %in% c("G1", "S", "G2")] <- NA
df$Phase <- phase
table(phase)

unlink(colpath, recursive=TRUE)
alabaster.base::saveObject(df, colpath)

We run some validation to ensure that our modified files are still valid.

library(alabaster.base)
validateObject(tmp)

# Confirming that the assay names changed.
readObject(tmp)$Phase

Session information {-}

sessionInfo()

LTLA/scRNAseq documentation built on June 28, 2024, 7:31 p.m.