Discriminating Probes Selection

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Documentation for package ‘disprose’ version 0.1.6

• DESCRIPTION file.
• Package NEWS.

Help Pages

add_adapters	Add adapters to probes
ann.data	Chlamydia pneumoniae genome annotation.
annotate_probes	Annotate probes
blast.fill	Local BLAST results with added content.
blast.raw	Local BLAST results.
blast_local	Local BLAST
count_GC	Calculate physical and chemical properties
count_MFE	Calculate physical and chemical properties
count_PhCh	Calculate physical and chemical properties
count_REP	Calculate physical and chemical properties
count_TM	Calculate physical and chemical properties
cut_probes	Cut probes
cut_string	Cut string into segments
delete_AcNum_version	Complement BLAST result
delete_duplicates_DF	Delete rows with duplicated values
delete_from_DB	Store data in SQLite database
fill_blast_result	Complement BLAST result
fill_blast_results	Complement BLAST result
get_GA_files	Read GISAID sequence file
get_GIs	Get GenInfo Identifier numbers
get_GIs_fix	Get GenInfo Identifier numbers
get_seq_for_DB	Get nucleotide sequences from NCBI
get_seq_for_DB_fix	Get nucleotide sequences from NCBI
get_seq_info	Get NCBI sequence record
get_seq_info_fix	Get NCBI sequence record
index_DB	Store data in SQLite database
info_listtodata	Get NCBI sequence record
list_DB	Store data in SQLite database
make_blast_DB	Builds local database for BLAST
make_ids	Create unique identification values
meta.all	Metadata of all available Chlamydia pneumoniae's sequences.
meta.target	Metadata of target Chlamydia pneumoniae's sequences.
normalize_DF	Normalize variable
rate_DF	Rate variables
read_and_unite_files	Read and unite files
read_from_DB	Store data in SQLite database
read_from_table_file	Read table file
store_in_DB	Store data in SQLite database
summarize_blast_result	Summarize BLAST result
trim_DF	Trim data frame
unite_NCBI_ac.nums	Assigns master record's id to all project records
unite_two_DF	Combine two data frames
write_to_DB	Store data in SQLite database