Mercurial > repos > greg > coral_multilocus_genotype
changeset 1:a690e0382ce4 draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 20 Sep 2019 09:17:28 -0400 |
| parents | adaf89535d2e |
| children | 9d0ddd9d62c5 |
| files | coral_multilocus_genotype.R |
| diffstat | 1 files changed, 15 insertions(+), 15 deletions(-) [+] |
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--- a/coral_multilocus_genotype.R Thu Aug 15 10:02:15 2019 -0400 +++ b/coral_multilocus_genotype.R Fri Sep 20 09:17:28 2019 -0400 @@ -200,9 +200,9 @@ # Rename the rn column. setnames(reference_alleles_data_table, c("rn"), c("affy_id")); # Rename the reference_alleles column. -setnames(reference_alleles_data_table, c("reference_alleles"), c("percent_reference_coral")); +setnames(reference_alleles_data_table, c("reference_alleles"), c("percent_acerv_coral")); # Round data to two digits. -reference_alleles_data_table$percent_reference_coral <- round(reference_alleles_data_table$percent_reference_coral, digits=2); +reference_alleles_data_table$percent_acerv_coral <- round(reference_alleles_data_table$percent_acerv_coral, digits=2); time_elapsed(start_time); # Alternative alleles @@ -218,9 +218,9 @@ # Rename the rn column. setnames(alternative_alleles_data_table, c("rn"), c("affy_id")); # Rename the alternative_alleles column. -setnames(alternative_alleles_data_table, c("alternative_alleles"), c("percent_alternative_coral")); +setnames(alternative_alleles_data_table, c("alternative_alleles"), c("percent_apalm_coral")); # Round data to two digits. -alternative_alleles_data_table$percent_alternative_coral <- round(alternative_alleles_data_table$percent_alternative_coral, digits=2); +alternative_alleles_data_table$percent_apalm_coral <- round(alternative_alleles_data_table$percent_apalm_coral, digits=2); time_elapsed(start_time); # The mlg_ids_data_table looks like this: @@ -305,15 +305,15 @@ select("affy_id", "percent_heterozygous_coral"), by="affy_id") %>% left_join(reference_alleles_data_table %>% - select("affy_id", "percent_reference_coral"), + select("affy_id", "percent_acerv_coral"), by="affy_id") %>% left_join(alternative_alleles_data_table %>% - select("affy_id", "percent_alternative_coral"), + select("affy_id", "percent_apalm_coral"), by="affy_id") %>% mutate(db_match = ifelse(is.na(db_match), "failed", db_match))%>% mutate(coral_mlg_clonal_id = ifelse(is.na(coral_mlg_clonal_id), "failed", coral_mlg_clonal_id)) %>% - mutate(genetic_coral_species_call = ifelse(percent_alternative_coral >= 40 & percent_alternative_coral <= 44.99, "A.palmata","other")) %>% - mutate(genetic_coral_species_call = ifelse(percent_alternative_coral >= 45 & percent_alternative_coral <= 51, "A.cervicornis", genetic_coral_species_call)) %>% + mutate(genetic_coral_species_call = ifelse(percent_apalm_coral >= 40 & percent_apalm_coral <= 44.99, "A.palmata","other")) %>% + mutate(genetic_coral_species_call = ifelse(percent_apalm_coral >= 45 & percent_apalm_coral <= 51, "A.cervicornis", genetic_coral_species_call)) %>% mutate(genetic_coral_species_call = ifelse(percent_heterozygous_coral > 40, "A.prolifera", genetic_coral_species_call)) %>% ungroup() %>% select(-group,-db_record); @@ -595,12 +595,12 @@ # NA NA PRO100175_PSU175_SAX_b02 P9SR10074 HG0227 # affy_id percent_missing_data_coral percent_heterozygous_coral # a550962-436.CEL 1.06 19.10 -# percent_reference_coral percent_alternative_coral +# percent_acerv_coral percent_apalm_coral # 40.10459 39.73396 sample_prep_data_frame <- affy_metadata_data_frame %>% left_join(stag_db_report %>% select("user_specimen_id", "affy_id", "percent_missing_data_coral", "percent_heterozygous_coral", - "percent_reference_coral", "percent_alternative_coral"), + "percent_acerv_coral", "percent_apalm_coral"), by='user_specimen_id'); # Get the number of rows for all data frames. num_rows <- nrow(sample_prep_data_frame); @@ -614,7 +614,7 @@ "public_after_date", "sperm_motility", "healing_time", "dna_extraction_method", "dna_concentration", "registry_id", "result_folder_name", "plate_barcode", "mlg", "affy_id", "percent_missing_data_coral", "percent_heterozygous_coral", - "percent_reference_coral", "percent_alternative_coral"); + "percent_acerv_coral", "percent_apalm_coral"); # Output the data frame for updating the alleles table. # Subset to only the new plate data. @@ -780,8 +780,8 @@ colnames(sample_table_data_frame) <- c("affy_id", "colony_location", "collection_date", "user_specimen_id", "registry_id", "depth", "dna_extraction_method", "dna_concentration", "public", "public_after_date", "percent_missing_data_coral", - "percent_missing_data_sym", "percent_reference_coral", - "percent_reference_sym", "percent_alternative_coral", + "percent_missing_data_sym", "percent_acerv_coral", + "percent_reference_sym", "percent_apalm_coral", "percent_alternative_sym", "percent_heterozygous_coral", "percent_heterozygous_sym", "field_call", "bcoral_genet_id"); for (i in 1:num_rows) { @@ -797,9 +797,9 @@ sample_table_data_frame$public_after_date[i] <- sample_prep_data_frame$public_after_date[i]; sample_table_data_frame$percent_missing_data_coral[i] <- sample_prep_data_frame$percent_missing_data_coral[i]; sample_table_data_frame$percent_missing_data_sym[i] <- DEFAULT_MISSING_NUMERIC_VALUE; - sample_table_data_frame$percent_reference_coral[i] <- sample_prep_data_frame$percent_reference_coral[i]; + sample_table_data_frame$percent_acerv_coral[i] <- sample_prep_data_frame$percent_acerv_coral[i]; sample_table_data_frame$percent_reference_sym[i] <- DEFAULT_MISSING_NUMERIC_VALUE; - sample_table_data_frame$percent_alternative_coral[i] <- sample_prep_data_frame$percent_alternative_coral[i]; + sample_table_data_frame$percent_apalm_coral[i] <- sample_prep_data_frame$percent_apalm_coral[i]; sample_table_data_frame$percent_alternative_sym[i] <- DEFAULT_MISSING_NUMERIC_VALUE; sample_table_data_frame$percent_heterozygous_coral[i] <- sample_prep_data_frame$percent_heterozygous_coral[i]; sample_table_data_frame$percent_heterozygous_sym[i] <- DEFAULT_MISSING_NUMERIC_VALUE;