Description Usage Arguments Author(s) References Examples
View source: R/make_threshold.R
This function calculate the best cutoff point of CMap score by using LINCS information file and user-determined true perturbation IDs. Before using this function, users must run init function only one time. Users set the output directory of init function as input directory of this function.
1 | make_threshold(pert_id_vec, cscore, cell, input.dir, output.dir)
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pert_id_vec |
character vector of pert_id, described in LINCS inst.info file. LINCS data containing this pert_id vector are considered as true hit in ROC analysis. |
cscore |
a object from cscore_calc function. |
cell |
character vector of cell_line, described in LINCS inst.info file naming a directory containing the result of init function. |
input.dir |
a character string naming a directory containing the result of init function. |
output.dir |
a character string naming a directory for output files from this function. |
Masaru Koido (masaru.koido@jfcr.or.jp)
M. Koido, et al., 'Detection of hub genes for developing gene expression networks under anticancer drug treatment', Oncotarget, 9(49), 29097-29111, 2018.
http://www.lincsproject.org/
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## Not run:
#-- only the first time of InDePTH
# init( input.dir = "input", out.dir = "init" )
#
# Run
res1 <- cscore_LINCS(up.sig = c( "217761_at", "217398_x_at", "218744_s_at" ),
dn.sig = c( "221856_s_at", "218193_s_at", "218457_s_at" ),
input.dir = "init",
output.dir = "output",
write.name = NULL)
make_threshold( pert_id_vec = c( "TRCN0000010389", "TRCN0000010390", "TRCN0000010391"),
cscore = res1,
cell = "HT29",
input.dir = "init",
output.dir = "output" )
## End(Not run)
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