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5_Master_Regulator_Inference.R
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5_Master_Regulator_Inference.R
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# # # # # # # # # # # # # # # # # # # # # # # # # # #
#
#
# Rafaella Sousa Ferraz <rafaellaferraz.16@hotmail.com>
#
# This script is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# This script is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
#
# # # # # # # # # # # # # # # # # # # # # # # # # # #
#Packages used in this analysis:
library(RTN)
#------------------------------ CREATE RTNA-OBJECT ----------------------------#
#EMAT-signature
rtna_emat_norm_met <- tni2tna.preprocess(object = rtni_55_sample,
phenotype = fold_crpc_norm_met,
hits = signature_emat$EMAT_genes)
rtna_emat_prim_met <- tni2tna.preprocess(object = rtni_55_sample,
phenotype = fold_crpc_prim_met,
hits = signature_emat$EMAT_genes)
rtna_emat_prim_norm <- tni2tna.preprocess(object = rtni_55_sample,
phenotype = fold_crpc_prim_norm,
hits = signature_emat$EMAT_genes)
#PCNA signature
rtna_pcna_norm_met <- tni2tna.preprocess(object = rtni_55_sample,
phenotype = fold_crpc_norm_met,
hits = pcna$SYMBOL)
rtna_pcna_prim_met <- tni2tna.preprocess(object = rtni_55_sample,
phenotype = fold_crpc_prim_met,
hits = pcna$SYMBOL)
rtna_pcna_prim_norm <- tni2tna.preprocess(object = rtni_55_sample,
phenotype = fold_crpc_prim_norm,
hits = pcna$SYMBOL)
#CRPC-signature
rtna_crpc_norm_met <- tni2tna.preprocess(object = rtni_55_sample,
phenotype = fold_crpc_norm_met,
hits = symbol_crpc_norm_met)
rtna_crpc_prim_met <- tni2tna.preprocess(object = rtni_55_sample,
phenotype = fold_crpc_prim_met,
hits = symbol_crpc_prim_met)
rtna_crpc_prim_norm <- tni2tna.preprocess(object = rtni_55_sample,
phenotype = fold_crpc_prim_norm,
hits = symbol_crpc_prim_norm)
#--------------------------- MASTER REGULATOR ANALYSIS ------------------------#
#EMAT-SIGNATURE
#metastatic x normal
rtna_emat_norm_met <- tna.mra(rtna_emat_norm_met, pValueCutoff = 0.01, pAdjustMethod = "BH",
minRegulonSize = 15, tnet = "dpi")
mra_emat_norm_met <- tna.get(rtna_emat_norm_met, what = "mra")
#metastatic x primary
rtna_emat_prim_met <- tna.mra(rtna_emat_prim_met, pValueCutoff = 0.01, pAdjustMethod = "BH",
minRegulonSize = 15, tnet = "dpi")
mra_emat_prim_met <- tna.get(rtna_emat_prim_met, what = "mra")
#primary x normal
rtna_emat_prim_norm <- tna.mra(rtna_emat_prim_norm, pValueCutoff = 0.01, pAdjustMethod = "BH",
minRegulonSize = 15, tnet = "dpi")
mra_emat_prim_norm <- tna.get(rtna_emat_prim_norm, what = "mra")
#PCNA-SIGNATURE
#metastatic x normal
rtna_pcna_norm_met <- tna.mra(rtna_pcna_norm_met, pValueCutoff = 0.01, pAdjustMethod = "BH",
minRegulonSize = 15, tnet = "dpi")
mra_pcna_norm_met <- tna.get(rtna_pcna_norm_met, what = "mra")
#metastatic x primary
rtna_pcna_prim_met <- tna.mra(rtna_pcna_prim_met, pValueCutoff = 0.01, pAdjustMethod = "BH",
minRegulonSize = 15, tnet = "dpi")
mra_pcna_prim_met <- tna.get(rtna_pcna_prim_met, what = "mra")
#primary x normal
rtna_pcna_prim_norm <- tna.mra(rtna_pcna_prim_norm, pValueCutoff = 0.01, pAdjustMethod = "BH",
minRegulonSize = 15, tnet = "dpi")
mra_pcna_prim_norm <- tna.get(rtna_pcna_prim_norm, what = "mra")
#CRPC-signature
#metastatic x normal
rtna_crpc_norm_met <- tna.mra(rtna_crpc_norm_met, pValueCutoff = 0.01, pAdjustMethod = "BH",
minRegulonSize = 15, tnet = "dpi")
mra_crpc_norm_met <- tna.get(rtna_crpc_norm_met, what = "mra")
#metastatic x primary
rtna_crpc_prim_met <- tna.mra(rtna_crpc_prim_met, pValueCutoff = 0.01, pAdjustMethod = "BH",
minRegulonSize = 15, tnet = "dpi")
mra_crpc_prim_met <- tna.get(rtna_crpc_prim_met, what = "mra")
#primary x normal
rtna_crpc_prim_norm<- tna.mra(rtna_crpc_prim_norm, pValueCutoff = 0.01, pAdjustMethod = "BH",
minRegulonSize = 15, tnet = "dpi")
mra_crpc_prim_norm <- tna.get(rtna_crpc_prim_norm, what = "mra")