Description Usage Arguments Details Value Note Author(s) Examples
Candidate genes from all methods can be plotted in an overview to identify overlapping signficant candidate genes using 'carpools.hit.overview'.
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wilcox |
Data output from 'stat.wilcox'. *Default* NULL *Values* Data output from 'stat.wilcox'. |
deseq |
Data output from 'stat.deseq'. *Default* NULL *Values* Data output from 'stat.deseq'. |
mageck |
Data output from 'stat.mageck'. *Default* NULL *Values* Data output from 'stat.mageck'. |
cutoff.deseq |
P-Value threshold used to determine significance. *Default* 0.001 *Values* numeric |
cutoff.wilcox |
P-Value threshold used to determine significance. *Default* 0.001 *Values* numeric |
cutoff.mageck |
P-Value threshold used to determine significance. *Default* 0.001 *Values* numeric |
cutoff.override |
Shall the p-value threshold be ignored? If this is TRUE, the top percentage gene of 'cutoff.hits' is used instead. *Default* FALSE *Values* TRUE, FALSE |
cutoff.hits |
The percentatge of top genes being used if 'cutoff.override=TRUE'. *Default** NULL *Values* numeric |
plot.genes |
Defines what kind of data is used. By default, overlapping genes are highlighted in red color. *Default* "overlapping" *Values* "overlapping" |
type |
Defines whether all genes are plotted or only those being enriched or depleted. *Default* "all" *Values* "all", "enriched", "depleted" |
none
Returns a generic plot.
none
Jan Winter
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | data(caRpools)
data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
control.picks=NULL)
data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
treated.list = list(TREAT1,TREAT2), namecolumn=1,
fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
fitType="parametric")
data.mageck = stat.mageck(untreated.list = list(CONTROL1, CONTROL2),
treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
norm.fun="median", extractpattern=expression("^(.+?)(_.+)"),
mageckfolder=NULL, sort.criteria="neg", adjust.method="fdr", filename = "TEST" , fdr.pval = 0.05)
carpools.hit.overview(wilcox=data.wilcox, deseq=data.deseq, mageck=data.mageck,
cutoff.deseq = 0.001, cutoff.wilcox = 0.05, cutoff.mageck = 0.05,
cutoff.override=FALSE, cutoff.hits=NULL, plot.genes="overlapping", type="enriched")
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