Updating pipeline to process Arabidopsis thaliana studies

[asaravia-butler]

@J-81 , at the end under this section:

Generate normalized expression matrix that includes annotations

norm_data_matrix_annotated <- oligo::exprs(norm_data) %>%

the last three lines of that command should be this:

dplyr::left_join(annot, by = c("ENSEMBL" = map_primary_keytypes[[unique(df_rs$organism)]])) %>% # Join with GeneLab Reference Annotation Table using key name expected in organism specific annotation table dplyr::mutate( count_ENSEMBL_mappings = ifelse(is.na(ENSEMBL), 0, count_ENSEMBL_mappings) ) %>% # Convert NA mapping to 0 dplyr::rename( !!map_primary_keytypes[[unique(df_rs$organism)]] := ENSEMBL )

Please make that change to this PR

[J-81]

@asaravia-butler Changed last three lines (c362fa5)