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choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
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SNPs from each pathway #108

Closed sarasaezALS closed 5 years ago

sarasaezALS commented 5 years ago

Hi again, thanks so much for your help. I am using the new version now and I have realize I didn't get a file .snps per each pathways (as I used to get with the older version). How can I recover rsID snp per each pathways?

choishingwan commented 5 years ago

Did you use --print-snp?

It should generate one single file which contains the information of each pathway, wtih Y indicate that the SNP is included in the pathway and N indicate that the SNP is not

On Tue, Apr 30, 2019 at 1:17 PM sarasaezALS notifications@github.com wrote:

Hi again, thanks so much for your help. I am using the new version now and I have realize I didn't get a file .snps per each pathways (as I used to get with the older version). How can I recover rsID snp per each pathways?

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sarasaezALS commented 5 years ago

ok, I used it and I got the file.snp. But I think something is missing from the file. This is how it looks like (just a few columns with N)

REACTOME_TRAF6_MEDIATED_INDUCTION_OF_TAK1_COMPLEX REACTOME_RIG_I_MDA5_MEDIATED_INDUCTION_OF_IFN_ALPHA_BETA_PATHWAYS REACTOME_IKK_COMPLEX_RECRUITMENT_MEDIATED_BY_RIP1 REACTOME_LIGAND_GATED_ION_CHANNEL_TRANSPORT REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER REACTOME_TRANSCRIPTIONAL_REGULATION_OF_WHITE_ADIPOCYTE_DIFFERENTIATION REACTOME_ENDOSOMAL_SORTING_COMPLEX_REQUIRED_FOR_TRANSPORT_ESCRT REACTOME_MEIOTIC_RECOMBINATION REACTOME_IL_2_SIGNALING REACTOME_IL_6_SIGNALING REACTOME_PLATELET_AGGREGATION_PLUG_FORMATION REACTOME_SIGNALING_BY_NOTCH REACTOME_LAGGING_STRAND_SYNTHESIS REACTOME_INTRINSIC_PATHWAY REACTOME_INHIBITION_OF_REPLICATION_INITIATION_OF_DAMAGED_DNA_BY_RB1_E2FREACTOME_ETHANOL_OXIDATION REACTOME_SYNTHESIS_OF_VERY_LONG_CHAIN_FATTY_ACYL_COAS REACTOME_DNA_REPLICATION REACTOME_CLEAVAGE_OF_GROWING_TRANSCRIPT_IN_THE_TERMINATIONREGION REACTOME_PKB_MEDIATED_EVENTS REACTOME_E2F_MEDIATED_REGULATION_OF_DNA_REPLICATION REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_HORMONE_SENSITIVE_LIPASE_HSL_MEDIATED_TRIACYLGLYCEROL_HYDROLYSIS REACTOME_SIGNALING_BY_INSULIN_RECEPTOR REACTOME_SIGNAL_ATTENUATION REACTOME_PURINE_METABOLISM REACTOME_SOS_MEDIATED_SIGNALLING REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER REACTOME_APOPTOSIS REACTOME_LIPID_DIGESTION_MOBILIZATION_AND_TRANSPORT REACTOME_HEMOSTASIS REACTOME_INFLUENZA_LIFE_CYCLE REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY REACTOME_HIV_INFECTION REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS REACTOME_HIV_LIFE_CYCLE REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT REACTOME_EARLY_PHASE_OF_HIV_LIFE_CYCLE REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLINGPROTEINS REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX REACTOME_RAF_MAP_KINASE_CASCADE REACTOME_VIRAL_MESSENGER_RNA_SYNTHESIS REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE REACTOME_SHC_MEDIATED_SIGNALLING REACTOME_INTERACTIONS_OF_VPR_WITH_HOST_CELLULAR_PROTEINS REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1 REACTOME_ACTIVATION_OF_ATR_IN_RESPONSE_TO_REPLICATION_STRESS REACTOME_UNWINDING_OF_DNA REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS REACTOME_GLUCURONIDATION REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C REACTOME_MYD88_MAL_CASCADE_INITIATED_ON_PLASMA_MEMBRANE REACTOME_INNATE_IMMUNE_SYSTEM REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN REACTOME_MITOTIC_PROMETAPHASE REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_CYCLIN_B REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1 REACTOME_LIPOPROTEIN_METABOLISM REACTOME_G1_S_SPECIFIC_TRANSCRIPTION REACTOME_THE_ROLE_OF_NEF_IN_HIV1_REPLICATION_AND_DISEASE_PATHOGENESIS REACTOME_CHYLOMICRON_MEDIATED_LIPID_TRANSPORT REACTOME_SIGNALING_BY_TGF_BETA_RECEPTOR_COMPLEXREACTOME_CONVERSION_FROM_APC_C_CDC20_TO_APC_C_CDH1_IN_LATE_ANAPHASE REACTOME_ACTIVATED_TLR4_SIGNALLING REACTOME_IMMUNE_SYSTEM REACTOME_BINDING_AND_ENTRY_OF_HIV_VIRION REACTOME_PHOSPHORYLATION_OF_THE_APC_C REACTOME_CYTOSOLIC_SULFONATION_OF_SMALL_MOLECULES REACTOME_INTEGRATION_OF_PROVIRUS REACTOME_GLUTATHIONE_CONJUGATION REACTOME_COMPLEMENT_CASCADE REACTOME_PHASE_II_CONJUGATION REACTOME_MTORC1_MEDIATED_SIGNALLING REACTOME_TOLL_RECEPTOR_CASCADES REACTOME_ACTIVATION_OF_BH3_ONLY_PROTEINS REACTOME_GLUCOSE_METABOLISM REACTOME_RNA_POL_III_CHAIN_ELONGATION REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS REACTOME_ADAPTIVE_IMMUNE_SYSTEM REACTOME_NOD1_2_SIGNALING_PATHWAY REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM REACTOME_MEIOTIC_SYNAPSIS REACTOME_ANTIGEN_PRESENTATION_FOLDING_ASSEMBLY_AND_PEPTIDE_LOADING_OF_CLASS_I_MHC REACTOME_THE_NLRP3_INFLAMMASOME REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX REACTOME_PIP3_ACTIVATES_AKT_SIGNALING REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION REACTOME_TANDEM_PORE_DOMAIN_POTASSIUM_CHANNELS REACTOME_INFLAMMASOMES REACTOME_POTASSIUM_CHANNELS REACTOME_NUCLEOTIDE_BINDING_DOMAIN_LEUCINE_RICH_REPEAT_CONTAINING_RECEPTOR_NLR_SIGNALING_PATHWAYS REACTOME_INWARDLY_RECTIFYING_K_CHANNELS REACTOME_AMYLOIDS REACTOME_PACKAGING_OF_TELOMERE_ENDS REACTOME_TELOMERE_MAINTENANCE REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION REACTOME_REMOVAL_OF_THE_FLAP_INTERMEDIATE_FROM_THE_C_STRAND REACTOME_CREATION_OF_C4_AND_C2_ACTIVATORS REACTOME_APC_CDC20_MEDIATED_DEGRADATION_OF_NEK2A REACTOME_INITIAL_TRIGGERING_OF_COMPLEMENT REACTOME_EXTENSION_OF_TELOMERES REACTOME_G2_M_CHECKPOINTS REACTOME_G2_M_DNA_DAMAGE_CHECKPOINT REACTOME_S_PHASE REACTOME_SCFSKP2_MEDIATED_DEGRADATION_OF_P27_P21 REACTOME_TRYPTOPHAN_CATABOLISM REACTOME_DNA_STRAND_ELONGATION REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY REACTOME_FGFR_LIGAND_BINDING_AND_ACTIVATION REACTOME_CHOLESTEROL_BIOSYNTHESIS REACTOME_APOBEC3G_MEDIATED_RESISTANCE_TO_HIV1_INFECTION REACTOME_GAP_JUNCTION_TRAFFICKING REACTOME_FGFR2C_LIGAND_BINDING_AND_ACTIVATION REACTOME_METABOLISM_OF_PORPHYRINS REACTOME_FGFR4_LIGAND_BINDING_AND_ACTIVATION REACTOME_VIF_MEDIATED_DEGRADATION_OF_APOBEC3G REACTOME_SIGNALING_BY_FGFR REACTOME_DIGESTION_OF_DIETARY_CARBOHYDRATE REACTOME_FGFR1_LIGAND_BINDING_AND_ACTIVATION REACTOME_GAP_JUNCTION_ASSEMBLY REACTOME_SYNTHESIS_OF_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI REACTOME_RNA_POL_I_TRANSCRIPTION_INITIATION REACTOME_PYRIMIDINE_METABOLISM REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS REACTOME_PI3K_CASCADE REACTOME_APOPTOTIC_EXECUTION_PHASE REACTOME_SHC_RELATED_EVENTS 1 rs3094315 752566 0.3615 Y N N N N N 1 rs11240777 798959 0.1832 Y N N N N N 1 rs117086422 845635 0.7913 Y N N N N N 1 rs57760052 845938 0.4934 Y N N N N N 1 rs28612348 846078 0.763 Y N N N N N 1 rs58781670 846398 0.7677 Y N N N N N 1 rs60454217 846465 0.1473 Y N N N N N 1 rs79396034 846543 0.2057 Y N N N N N 1 rs4475691 846808 0.855 Y N N N N N

choishingwan commented 5 years ago

Ok, this is definitely a bug then. I am currently test running the latest version. Will let you know once that's ready. Should solve most of the problems that you've encountered so far (I hope).

On Tue, Apr 30, 2019 at 2:13 PM sarasaezALS notifications@github.com wrote:

ok, I used it and I got the file.snp. But I think something is missing from the file. This is how it looks like (just a few columns with N)

REACTOME_TRAF6_MEDIATED_INDUCTION_OF_TAK1_COMPLEX REACTOME_RIG_I_MDA5_MEDIATED_INDUCTION_OF_IFN_ALPHA_BETA_PATHWAYS REACTOME_IKK_COMPLEX_RECRUITMENT_MEDIATED_BY_RIP1 REACTOME_LIGAND_GATED_ION_CHANNEL_TRANSPORT REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER REACTOME_TRANSCRIPTIONAL_REGULATION_OF_WHITE_ADIPOCYTE_DIFFERENTIATION REACTOME_ENDOSOMAL_SORTING_COMPLEX_REQUIRED_FOR_TRANSPORT_ESCRT REACTOME_MEIOTIC_RECOMBINATION REACTOME_IL_2_SIGNALING REACTOME_IL_6_SIGNALING REACTOME_PLATELET_AGGREGATION_PLUG_FORMATION REACTOME_SIGNALING_BY_NOTCH REACTOME_LAGGING_STRAND_SYNTHESIS REACTOME_INTRINSIC_PATHWAY REACTOME_INHIBITION_OF_REPLICATION_INITIATION_OF_DAMAGED_DNA_BY_RB1_E2FREACTOME_ETHANOL_OXIDATION REACTOME_SYNTHESIS_OF_VERY_LONG_CHAIN_FATTY_ACYL_COAS REACTOME_DNA_REPLICATION REACTOME_CLEAVAGE_OF_GROWING_TRANSCRIPT_IN_THE_TERMINATIONREGION REACTOME_PKB_MEDIATED_EVENTS REACTOME_E2F_MEDIATED_REGULATION_OF_DNA_REPLICATION REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_HORMONE_SENSITIVE_LIPASE_HSL_MEDIATED_TRIACYLGLYCEROL_HYDROLYSIS REACTOME_SIGNALING_BY_INSULIN_RECEPTOR REACTOME_SIGNAL_ATTENUATION REACTOME_PURINE_METABOLISM REACTOME_SOS_MEDIATED_SIGNALLING REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER REACTOME_APOPTOSIS REACTOME_LIPID_DIGESTION_MOBILIZATION_AND_TRANSPORT REACTOME_HEMOSTASIS REACTOME_INFLUENZA_LIFE_CYCLE REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY REACTOME_HIV_INFECTION REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS REACTOME_HIV_LIFE_CYCLE REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT REACTOME_EARLY_PHASE_OF_HIV_LIFE_CYCLE REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLINGPROTEINS REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX REACTOME_RAF_MAP_KINASE_CASCADE REACTOME_VIRAL_MESSENGER_RNA_SYNTHESIS REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE REACTOME_SHC_MEDIATED_SIGNALLING REACTOME_INTERACTIONS_OF_VPR_WITH_HOST_CELLULAR_PROTEINS REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1 REACTOME_ACTIVATION_OF_ATR_IN_RESPONSE_TO_REPLICATION_STRESS REACTOME_UNWINDING_OF_DNA REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS REACTOME_GLUCURONIDATION REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C REACTOME_MYD88_MAL_CASCADE_INITIATED_ON_PLASMA_MEMBRANE REACTOME_INNATE_IMMUNE_SYSTEM REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN REACTOME_MITOTIC_PROMETAPHASE REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_CYCLIN_B REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1 REACTOME_LIPOPROTEIN_METABOLISM REACTOME_G1_S_SPECIFIC_TRANSCRIPTION REACTOME_THE_ROLE_OF_NEF_IN_HIV1_REPLICATION_AND_DISEASE_PATHOGENESIS REACTOME_CHYLOMICRON_MEDIATED_LIPID_TRANSPORT REACTOME_SIGNALING_BY_TGF_BETA_RECEPTOR_COMPLEXREACTOME_CONVERSION_FROM_APC_C_CDC20_TO_APC_C_CDH1_IN_LATE_ANAPHASE REACTOME_ACTIVATED_TLR4_SIGNALLING REACTOME_IMMUNE_SYSTEM REACTOME_BINDING_AND_ENTRY_OF_HIV_VIRION REACTOME_PHOSPHORYLATION_OF_THE_APC_C REACTOME_CYTOSOLIC_SULFONATION_OF_SMALL_MOLECULES REACTOME_INTEGRATION_OF_PROVIRUS REACTOME_GLUTATHIONE_CONJUGATION REACTOME_COMPLEMENT_CASCADE REACTOME_PHASE_II_CONJUGATION REACTOME_MTORC1_MEDIATED_SIGNALLING REACTOME_TOLL_RECEPTOR_CASCADES REACTOME_ACTIVATION_OF_BH3_ONLY_PROTEINS REACTOME_GLUCOSE_METABOLISM REACTOME_RNA_POL_III_CHAIN_ELONGATION REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS REACTOME_ADAPTIVE_IMMUNE_SYSTEM REACTOME_NOD1_2_SIGNALING_PATHWAY REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM REACTOME_MEIOTIC_SYNAPSIS REACTOME_ANTIGEN_PRESENTATION_FOLDING_ASSEMBLY_AND_PEPTIDE_LOADING_OF_CLASS_I_MHC REACTOME_THE_NLRP3_INFLAMMASOME REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX REACTOME_PIP3_ACTIVATES_AKT_SIGNALING REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION REACTOME_TANDEM_PORE_DOMAIN_POTASSIUM_CHANNELS REACTOME_INFLAMMASOMES REACTOME_POTASSIUM_CHANNELS REACTOME_NUCLEOTIDE_BINDING_DOMAIN_LEUCINE_RICH_REPEAT_CONTAINING_RECEPTOR_NLR_SIGNALING_PATHWAYS REACTOME_INWARDLY_RECTIFYING_K_CHANNELS REACTOME_AMYLOIDS REACTOME_PACKAGING_OF_TELOMERE_ENDS REACTOME_TELOMERE_MAINTENANCE REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION REACTOME_REMOVAL_OF_THE_FLAP_INTERMEDIATE_FROM_THE_C_STRAND REACTOME_CREATION_OF_C4_AND_C2_ACTIVATORS REACTOME_APC_CDC20_MEDIATED_DEGRADATION_OF_NEK2A REACTOME_INITIAL_TRIGGERING_OF_COMPLEMENT REACTOME_EXTENSION_OF_TELOMERES REACTOME_G2_M_CHECKPOINTS REACTOME_G2_M_DNA_DAMAGE_CHECKPOINT REACTOME_S_PHASE REACTOME_SCFSKP2_MEDIATED_DEGRADATION_OF_P27_P21 REACTOME_TRYPTOPHAN_CATABOLISM REACTOME_DNA_STRAND_ELONGATION REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY REACTOME_FGFR_LIGAND_BINDING_AND_ACTIVATION REACTOME_CHOLESTEROL_BIOSYNTHESIS REACTOME_APOBEC3G_MEDIATED_RESISTANCE_TO_HIV1_INFECTION REACTOME_GAP_JUNCTION_TRAFFICKING REACTOME_FGFR2C_LIGAND_BINDING_AND_ACTIVATION REACTOME_METABOLISM_OF_PORPHYRINS REACTOME_FGFR4_LIGAND_BINDING_AND_ACTIVATION REACTOME_VIF_MEDIATED_DEGRADATION_OF_APOBEC3G REACTOME_SIGNALING_BY_FGFR REACTOME_DIGESTION_OF_DIETARY_CARBOHYDRATE REACTOME_FGFR1_LIGAND_BINDING_AND_ACTIVATION REACTOME_GAP_JUNCTION_ASSEMBLY REACTOME_SYNTHESIS_OF_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI REACTOME_RNA_POL_I_TRANSCRIPTION_INITIATION REACTOME_PYRIMIDINE_METABOLISM REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS REACTOME_PI3K_CASCADE REACTOME_APOPTOTIC_EXECUTION_PHASE REACTOME_SHC_RELATED_EVENTS 1 rs3094315 752566 0.3615 Y N N N N N 1 rs11240777 798959 0.1832 Y N N N N N 1 rs117086422 845635 0.7913 Y N N N N N 1 rs57760052 845938 0.4934 Y N N N N N 1 rs28612348 846078 0.763 Y N N N N N 1 rs58781670 846398 0.7677 Y N N N N N 1 rs60454217 846465 0.1473 Y N N N N N 1 rs79396034 846543 0.2057 Y N N N N N 1 rs4475691 846808 0.855 Y N N N N N

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sarasaezALS commented 5 years ago

Great! I was using an older version and I never had any other problem with it. For publication quality I just wanted to do it with the last version.

choishingwan commented 5 years ago

Btw, this problem should've been fixed on v2.2.0