rm_dups: Remove Duplicate Gene Entries The purpose. of this function...

In jgockley62/igraphNetworkExpansion: Trace Subnetworks from an AD Necortical Network of Protein-Protein Interactions

Remove Duplicate Gene Entries The purpose. of this function is to pull info from a synapse table into a dataframe. Removal can be of all entries with a lower score in a given column or entries which lack the desired ensg

Description

Remove Duplicate Gene Entries The purpose. of this function is to pull info from a synapse table into a dataframe. Removal can be of all entries with a lower score in a given column or entries which lack the desired ensg

Usage

rm_dups(df, feature_col, feature, type, type_spec, ensg_keep = NULL)

Arguments

df	the data frame of gene names
feature_col	the column of the feature to treat as rows ie.'GName'
feature	the values of the feature to pull ie. NPC1
type	highest value or ensg ie 'value' or 'ensg'
type_spec	column name of type ie 'ENSG' or 'Overall'
ensg_keep	the ensg to retain if method is ensg default = NULL

Value

a dataframe object

Examples

## Not run: 
 syn <- log_into_synapse()
 omics_scores <- dplyr::left_join(
  table_pull(
    syn_id ='syn25575156',
    feature_name = 'GeneName',
    features = names(igraph::V(net)),
    column_names = c('ENSG', 'OmicsScore', 'GeneticsScore', 'Logsdon'),
    synap_import = syn$synapse
  ), 
  table_pull(
    syn_id ='syn22758536',
    feature_name = 'GName',
    features = names(igraph::V(net)),
    column_names = c('ENSG', 'GName', 'RNA_TE', 'Pro_TE'),
    synap_import = syn$synapse
  ), 
  by = 'ENSG'
 )
 colnames(omics_scores)[ colnames(omics_scores) == 'Logsdon' ] <- 'Overall'
 omics_scores <- rm_dups(
   df = omics_scores,
   feature_col = 'GName',
   feature = 'POLR2J3',
   type = 'value',
   type_spec = 'Overall' ,
   ensg_keep = NULL
 )
 omics_scores <- rm_dups(
    df = omics_scores,
    feature_col = 'GName',
    feature = "FCGBP",
    type = 'ensg',
    type_spec = 'ENSG' ,
    ensg_keep = 'ENSG00000281123'
 )

## End(Not run)

jgockley62/igraphNetworkExpansion documentation built on April 15, 2022, 12:14 a.m.