predict_PLSR_graph: Predict all files in a folder using PLSR of a training...

In graeberlab/small.cell.project: small.cell.project

Description

Predict all files in a folder using PLSR of a training dataset, file names have to be of form name_.......txt Predicts classifications of test dataset and writes out predictions

Usage

predict_PLSR_graph(prediction_file, test_files_folder, anno.file,
  output_folder = "./", train_string = "", test_pattern = "",
  train_pattern = "", comps = 3, varimax = F, varimax.comp = 2,
  shape.palette = NULL, colpalette = NULL)

Arguments

prediction_file	file with training data features rows , genes columns, features are in column 1
test_files_folder	folder of test files
anno.file	Annotation file, first column is sample names, 2nd is annotation
output_folder	output folder
train_string	string of training data to insert in file name of predicted scores
train_pattern	annotation type of main group in your comparison ,taken from 2nd column in anno.
comps	number of components to compute
varimax.comp	# of varimax comps , has to match # of comps
shape.palette	vector with numbers reprsenting shapes according to R plotting
test_string	string of data being tested to insert in file name of predicted scores
varimax.it	do you want to perform varimax , default varimax=F

graeberlab/small.cell.project documentation built on May 12, 2019, 5:16 p.m.