Description Usage Arguments Author(s)
Wrapper function to run saarclust pipeline for a given number of long reads reads.
1 2 3 4 5 |
minimap.file |
A path to the minimap file to load. |
outputfolder |
A folder name to export the results. |
num.clusters |
Expected number of clusters. (for 22 autosomes == 44 clusters) |
EM.iter |
Number of iteration to run EM for. |
alpha |
Estimated level of background in Strand-seq reads. |
minLib |
Minimal number of StrandS libraries being represent per long PB read |
upperQ |
Filter out given percentage of PacBio reads with the highest number of alignments. |
theta.param |
A |
pi.param |
A |
logL.th |
Set the difference between objective function from the current and the previous interation for EM algorithm to converge. |
theta.constrain |
Recalibrate theta values to meet expected distribution of W and C strand across Strand-seq libraries. |
store.counts |
Logical if to store raw read counts per PB read |
HC.input |
Filaname where hard clustering results are stored |
cellNum |
Specifies the number of single cells to be used in clustering |
David Porubsky
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