View source: R/prepare_libraries_sop_merged.R
prepare_libraries_sop_merged | R Documentation |
This function prepares the libraries made of all sub-libraries containing structure-organism pairs
prepare_libraries_sop_merged(
files = get_params(step = "prepare_libraries_sop_merged")$files$libraries$sop$prepared,
filter = get_params(step = "prepare_libraries_sop_merged")$organisms$filter$mode,
level = get_params(step = "prepare_libraries_sop_merged")$organisms$filter$level,
value = get_params(step = "prepare_libraries_sop_merged")$organisms$filter$value,
output_key = get_params(step =
"prepare_libraries_sop_merged")$files$libraries$sop$merged$keys,
output_org_tax_ott = get_params(step =
"prepare_libraries_sop_merged")$files$libraries$sop$merged$organisms$taxonomies$ott,
output_str_stereo = get_params(step =
"prepare_libraries_sop_merged")$files$libraries$sop$merged$structures$stereo,
output_str_met = get_params(step =
"prepare_libraries_sop_merged")$files$libraries$sop$merged$structures$metadata,
output_str_nam = get_params(step =
"prepare_libraries_sop_merged")$files$libraries$sop$merged$structures$names,
output_str_tax_cla = get_params(step =
"prepare_libraries_sop_merged")$files$libraries$sop$merged$structures$taxonomies$cla,
output_str_tax_npc = get_params(step =
"prepare_libraries_sop_merged")$files$libraries$sop$merged$structures$taxonomies$npc
)
files |
List of libraries to be merged |
filter |
Boolean. TRUE or FALSE if you want to filter the library |
level |
Biological rank to be filtered. Kingdom, phylum, family, genus, ... |
value |
Name of the taxon or taxa to be kept, e.g. 'Gentianaceae|Apocynaceae' |
output_key |
Output file for keys |
output_org_tax_ott |
Output file for organisms taxonomy (OTT) |
output_str_stereo |
Output file for structures stereo |
output_str_met |
Output file for structures metadata |
output_str_nam |
Output file for structures names |
output_str_tax_cla |
Output file for structures taxonomy (Classyfire) |
output_str_tax_npc |
Output file for structures taxonomy (NPC) |
It can be restricted to specific taxa to have more biologically meaningful annotation.
NULL
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