anovaLike | R Documentation |
This function executes in a docker edgeR for the idnetification of differentially expressed genes in single-cells RNAseq
anovaLike(
group = c("sudo", "docker"),
file,
sep,
cluster.file,
ref.cluster,
logFC.threshold = 1,
FDR.threshold,
logCPM.threshold = 4,
plot = c(TRUE, FALSE)
)
group |
a character string. Two options: sudo or docker, depending to which group the user belongs |
file |
a character string indicating the counts table file with the path of the file. |
sep |
separator used in count file, e.g. '\t', ',' |
cluster.file |
a character string indicating the _clustering.output.txt file of interest, generated by bootstrapSimlar or bootStrapTsne. IMPORTANT this file miust be located in the same folder where counts.table is placed |
ref.cluster |
a number indicating the cluster to be used a reference for anova-like comparison with the other clusters. |
logFC.threshold |
minimal logFC present in at least one of the comparisons with respect to reference covariate |
FDR.threshold |
minimal FDR present in at least one of the comparisons with respect to reference covariate |
logCPM.threshold |
minimal average abundance |
plot |
boolean, TRUE a plot of differentially expressed genes is generated |
Three tab delimited files file with prefix DE\_, filtered\_DE\_, logFC\_filtered\_DE\_ followed by the counts table name, the count table, reordered on the basis of cluster positions, has the extension \_reordered.txt
Raffaele Calogero, raffaele.calogero [at] unito [dot] it, University of Torino, Italy
## Not run:
#running deDetection
system("wget http://130.192.119.59/public/annotated_setPace_10000_noC5_clustering.output.txt")
system("wget http://130.192.119.59/public/annotated_setPace_10000_noC5.txt.zip")
unzip("annotated_setPace_10000_noC5.txt.zip")
anovaLike(group="docker", file=paste(getwd(),"annotated_setPace_10000_noC5.txt",sep="/"),
sep="\t", cluster.file="annotated_setPace_10000_noC5_clustering.output.txt", ref.cluster=3,
logFC.threshold=1, FDR.threshold=0.05, logCPM.threshold=4, plot=TRUE)
## End(Not run)
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