readDesignMergeCel: Read the cell type study metadata file and create the RMA...

In PavlidisLab/neuroExpressoAnalysis: Marker genes of brain cell types and their use in analysis of whole tissue data

Read the cell type study metadata file and create the RMA normalized expression matrix.

Description

This function reads the study design file 'data-raw/Mouse_Cell_Type_Data/cellTypeStudies.tsv' included in the package and cel files pointed in the file to create the RMA normalized expression matrix. The products of this function are already loaded with the package. Use only for replication or upon editing cellTypeStudies.tsv for personal use.

Usage

  readDesignMergeCel(desFile = "data-raw/Mouse_Cell_Type_Data/cellTypeStudies.tsv",
  gsm = "samples", normalize,
  celRegex = "(GSM.*?(?=,|$))|(PC\\d....)|(Y[+].*?((?=(,))|\\d+))|((?<=:)|(?<=[,]))A((9)|(10))_[0-9]{1,}_Chee_S1_M430A|(v2_(?![G,H,r]).*?((?=(,))|($)))|(SSC.*?((?=(,))|($)))|(MCx.*?((?=(,))|($)))|(Cbx.*?((?=(,))|($)))",
  celDir = "data-raw/cel/", expFile, desOut,
  gemmaDir = "data-raw/GemmaAnnots")

Arguments

desFile	Address of the study metadata file
gsm	column name that has the GSM identifiers of the samples. The identifiers must be sperated by commas
normalize	The column name that marks which studies should be included.
celRegex	Regular expression that picks the sample names from the gsm column. Default option is for the cellTypeStudies.tsv. Any modifications to the file should not require changes to the default as long as they are samples from GEO with GSM identifiers. If files that are named differently are added, modify the regex to recognize them.
expFile	name of the output file for gene expression. The file will be a csv
desOut	name of the output file for sample metadata. The file will be a tsv
gemmaDir	The directory that houses the gemma annotations that are created by getGemmaAnnot

PavlidisLab/neuroExpressoAnalysis documentation built on Aug. 23, 2022, 7:42 a.m.