#Error. Could not read input tissue database.

[hust-yyan]

Hi, I recently performed a TWAS study on miRNA expression. After creating the predict database using our miRNA expression and genotype data, we encountered the following error during s-Predixcan analysis.

Here is the code I used to create the Predict database
library(DBI)
library(RSQLite)
"%&%" <- function(a,b) paste(a,b, sep='')
driver <- dbDriver('SQLite')
model_summaries <- read.table('./summary/Model_training_chr1_model_summaries_filter.txt',header = T, stringsAsFactors = F)
tiss_summary <- read.table('./summary/Model_training_chr1_summary.txt', header = T, stringsAsFactors = F)
n_samples <- tiss_summary$n_samples
for (i in 2:22) {
model_summaries <- rbind(model_summaries,
read.table('./summary/Model_training_chr'%&%as.character(i) %&% '_model_summaries_filter.txt', header = T, stringsAsFactors = F))
tiss_summary <- rbind(tiss_summary,
read.table('./summary/Model_training_chr' %&% as.character(i) %&% '_summary.txt', header = T, stringsAsFactors = F))
}
model_summaries <- rename(model_summaries, gene = gene_id)

Create a database connection

conn <- dbConnect(drv = driver, './dbs/miRNA_expression_204.db')
dbWriteTable(conn, 'model_summaries', model_summaries, overwrite = TRUE)
dbExecute(conn, "CREATE INDEX gene_model_summary ON model_summaries (gene)")

Weights Table -----

weights <- read.table('./weights/Model_training_chr1_weights.txt', header = T,stringsAsFactors = F)
for (i in 2:22) {
weights <- rbind(weights,
read.table('./weights/Model_training_chr' %&% as.character(i) %&% '_weights.txt', header = T, stringsAsFactors = F))

}
weights <- rename(weights, gene = gene_id)
dbWriteTable(conn, 'weights', weights, overwrite = TRUE)
dbExecute(conn, "CREATE INDEX weights_rsid ON weights (rsid)")
dbExecute(conn, "CREATE INDEX weights_gene ON weights (gene)")
dbExecute(conn, "CREATE INDEX weights_rsid_gene ON weights (rsid, gene)")

Sample_info Table ----

sample_info <- data.frame(n_samples = n_samples, population = 'EAS') # Provide the population info
dbWriteTable(conn, 'sample_info', sample_info, overwrite = TRUE)

Construction Table ----

construction <- tiss_summary %>%
select(chrom, cv_seed) %>%
rename(chromosome = chrom)
dbWriteTable(conn, 'construction', construction, overwrite = TRUE)
dbDisconnect(conn)

[Fnyasimi]

Hi @hust-yyan can you share the command you are using to run SPrediXcan and the full error log? Also add --verbosity 1 and --throw to log in more run info.

[hust-yyan]

Thanks for your quick reply!
this is my command to run SPrediXcan:
/home/yyan/software/MetaXcan/software/SPrediXcan.py
--model_db_path ./input/miRNA_expression_204.db
--covariance ./input/Model_training_covariances.txt.gz
--gwas_folder /data1/yyan_tmp/miRNA_eqtl/TWAS/GWAS_data
--gwas_file_pattern "${trait}.auto.rsq07.mac10.txt.gz"
--snp_column SNPID
--effect_allele_column Allele2
--non_effect_allele_column Allele1
--beta_column BETA
--se_column SE
--pvalue_column p.value
--output_file ./results/${trait}_TAWS.csv
--verbosity 1
--throw

and this is the error info

And I didn't find the weight column in the weights file, which is the weight file generated by PredictDB.

[Fnyasimi]

@hust-yyan the beta is the weight. You need the right columns in your weights table in the db.

weights <- weights %>%
       dplyr::rename(gene = gene_id, ref_allele = ref, eff_allele = alt, weight = beta)

[hust-yyan]

Hello, my previous problem has been solved. Now the program can run successfully.But there was a warning.He said that these three genes skipped. I checked weights file and found that weights of two genes were missing. Is this normal?

[Fnyasimi]

That's not normal. I would advice you to look back at your filtering/QC step if everything worked well.