xMLrename: Function to rename predictors used in machine learning

In Pi: Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

Description

xMLrename is supposed to rename predictors used in machine learning. It returns an object of class "sTarget".

Usage

xMLrename(sTarget, old_names, new_names)

Arguments

sTarget	an object of class "sTarget"
old_names	a vector for the original names of predictors to be renamed
new_names	a vector for the new names

Value

an object of class "sTarget"

Note

none

See Also

xMLrename

Examples

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
old_names <- colnames(sTarget$predictor)[-c(1,2)]
old_names_1 <- c('nGene_20000_constant', 'eGene_CD14', 'eGene_LPS2',
'eGene_LPS24', 'eGene_IFN', 'eGene_Bcell', 'eGene_CD4', 'eGene_CD8',
'eGene_Neutrophil', 'eGene_NK', 'eGene_Blood', 'cGene_Monocytes',
'cGene_Macrophages_M0', 'cGene_Macrophages_M1', 'cGene_Macrophages_M2',
'cGene_Neutrophils', 'cGene_Naive_CD4_T_cells',
'cGene_Total_CD4_T_cells', 'cGene_Naive_CD8_T_cells',
'cGene_Total_CD8_T_cells', 'cGene_Naive_B_cells',
'cGene_Total_B_cells', 'dGene', 'pGene', 'fGene')
old_names_2 <- c('nGene_20000_constant', 'eGene_Pi_eQTL_CD14',
'eGene_Pi_eQTL_LPS2', 'eGene_Pi_eQTL_LPS24', 'eGene_Pi_eQTL_IFN',
'eGene_Pi_eQTL_Bcell', 'eGene_Pi_eQTL_CD4', 'eGene_Pi_eQTL_CD8',
'eGene_Pi_eQTL_Neutrophil', 'eGene_Pi_eQTL_NK', 'eGene_Pi_eQTL_Blood',
'cGene_Monocytes', 'cGene_Macrophages_M0', 'cGene_Macrophages_M1',
'cGene_Macrophages_M2', 'cGene_Neutrophils', 'cGene_Naive_CD4_T_cells',
'cGene_Total_CD4_T_cells', 'cGene_Naive_CD8_T_cells',
'cGene_Total_CD8_T_cells', 'cGene_Naive_B_cells',
'cGene_Total_B_cells', 'dGene', 'pGene', 'fGene')
new_names <- c('nearbyGenes_nGene: nearby genes', 'eQTL_eGene: resting
state (CD14+)', 'eQTL_eGene: activating state (CD14+ by LPS2h)',
'eQTL_eGene: activating state (CD14+ by LPS24h)', 'eQTL_eGene:
activating state (CD14+ by IFN24h)', 'eQTL_eGene: B cells',
'eQTL_eGene: CD4+ T cells', 'eQTL_eGene: CD8+ T cells', 'eQTL_eGene:
neutrophils', 'eQTL_eGene: NK cells','eQTL_eGene: peripheral blood',
'HiC_cGene: monocytes', 'HiC_cGene: macrophages (M0)', 'HiC_cGene:
macrophages (M1)', 'HiC_cGene: macrophages (M2)', 'HiC_cGene:
neutrophils', 'HiC_cGene: CD4+ T cells (naive)', 'HiC_cGene: CD4+ T
cells (total)', 'HiC_cGene: CD8+ T cells (naive)', 'HiC_cGene: CD8+ T
cells (total)', 'HiC_cGene: B cells (naive)', 'HiC_cGene: B cells
(total)', 'Annotation_dGene: disease genes', 'Annotation_pGene:
phenotype genes', 'Annotation_fGene: function genes')
sTarget_renamed <- xMLrename(sTarget, old_names_1, new_names)
sTarget_renamed <- xMLrename(sTarget_renamed, old_names_2, new_names)

## End(Not run)

Pi documentation built on Nov. 26, 2020, 2:01 a.m.