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Prepare PTM-SEA input

Source: R/gsea.R
prepare_ptmsea_input.Rd

Write a GCT file with timewise differential analysis t-scores as values and human flanking sequences as IDs. rat_to_human_ptm_map is used to map from rat to human phosphosites, and a human protein FASTA file is used to add human flanking sequences.

Usage

prepare_ptmsea_input(
  tissue = NULL,
  fasta = NULL,
  rat_to_human_ptm_map = MotrpacRatTraining6moData::RAT_TO_HUMAN_PHOSPHO,
  outdir = ".",
  outfile_prefix = NULL,
  input = NULL,
  cast_vars = c("sex", "comparison_group")
)

Arguments

tissue

character, tissue abbreviation, one of MotrpacRatTraining6moData::TISSUE_ABBREV. Must be specified if cusotm input is not provided.

fasta

Biostrings::XStringSet object returned from reading in a human protein FASTA file with Biostrings::readAAStringSet(). Names of the Biostrings::XStringSet object should be set to the human protein accession, e.g., "Q96QG7". If not specified, the result of load_uniprot_human_fasta() is used, which returns the version of the UniProt human protein FASTA used in the manuscript.

rat_to_human_ptm_map

data frame with columns "ptm_id_rat_refseq" and "ptm_id_human_uniprot" used to map PTMs from rat to human. Default: MotrpacRatTraining6moData::RAT_TO_HUMAN_PHOSPHO

outdir

character, output directory for GCT file. The directory is created if it does not already exist. Current directory by default.

outfile_prefix

character, prefix for output GCT file. By default, this prefix includes the specified tissue and current date. Must be specified for custom input data.

input

optional data frame if the user wants to perform this analysis for a custom set of differential analysis results. Required columns are "feature_ID", "tscore", and cast_vars.

cast_vars

character vector of column names in the differential analysis results that are used to convert the table from long to wide format, with t-scores as the value variable. See tidyr::pivot_wider() for more details. Default: "sex", "comparison_group"

Value

character, full path to GCT file

See also

load_uniprot_human_fasta(), find_flanks(), MotrpacRatTraining6moData::RAT_TO_HUMAN_PHOSPHO

Examples

if (FALSE) {
# Using existing differential analysis results
prepare_ptmsea_input("HEART", outdir="/tmp")

# Using a "custom" input
res = combine_da_results(tissues = "HEART", assays = "PHOSPHO")
# add dummy column
prepare_ptmsea_input(input=res, outdir="/tmp", outfile_prefix="HEART_PHOSPHO")
}