Description Usage Arguments Value Author(s) Examples
View source: R/DENDRO_helper.R
This function filter out low expressed gene (cut.off.VAF) and high dropout cells (cut.off.sd) based on read counts and plot out the summary distributions.
1 | FilterCellMutation(X, N, Z, Info = NULL, label = NULL, cut.off.VAF = 0.05, cut.off.sd = 5, plot = TRUE)
|
X |
An matrix contains variants allele read counts across cell (column) and loci (row). |
N |
An matrix contains total allele read counts across cell (column) and loci (row). |
Z |
An mutation indicator matrix (1 for mutation, 0 for normal) across cell (column) and loci (row). |
Info |
Mutation loci information. Matrix with row number same to number of loci and column number > 1. This is optional. Default NULL |
label |
An integer 1D vector that decide the label color by type. The label can be assigned due to piror information such as individuals or site. Default NULL, where no color label. |
cut.off.VAF |
Variant allele frequency (VAF, sum(Z)/length(Z) ) filter threshold. Variants with variants allele frequency less than cut.off.VAF (too rare) or greater than 1-cut.off.VAF (too common) are filtered out. Default 0.05 |
cut.off.sd |
Cell total expression (sum(N)) filter threshold. Cells with total expression less than mean(N)-cut.off.sd*sd(N) (too small) or greater than mean(N)+cut.off.sd*sd(N) (double or triplet) are filtered out. Default 5 |
plot |
TRUE or FALSE, decide whether to plot the distribution and cut off (red line). Default value is TRUE. |
List of filtered matrix
X |
Input X after filtering |
N |
Input N after filtering |
Z |
Input Z after filtering |
Info |
Input Info after filtering |
label |
Input label after filtering |
Zilu Zhou
1 2 |
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