postCounts: post counts to database

In BrentLab/brentlabRnaSeqTools: Management/QC for brentlab RNAseq data

post counts to database

Description

using the package httr, post the raw count .csv, which is the compiled counts for a given run, to the database

Usage

postCounts(
  database_counts_url,
  run_number,
  auth_token,
  count_df,
  fastq_table,
  count_file_suffix = "_read_count.tsv"
)

Arguments

database_counts_url	eg database_info$kn99_urls$Counts. See database_info
run_number	the run number of this counts sheet – this is important b/c fastqFileNames aren't necessarily unique outside of their runs
auth_token	see getUserAuthToken
count_df	the counts read in as a dataframe. Make sure there is no 'feature' or 'gene_id' column. Colnames need to be the sample identifier
fastq_table	a recent pull of the database fastq table
count_file_suffix	the suffix appended to the fastqFileName in the count file column headings. default is "_read_count.tsv"

Value

a list of httr::response() objects

BrentLab/brentlabRnaSeqTools documentation built on Aug. 20, 2023, 9:22 a.m.