View source: R/calculate_sig_score.R
calculate_sig_score_pca | R Documentation |
Calculating signature score using PCA method
calculate_sig_score_pca(
pdata = NULL,
eset,
signature,
mini_gene_count = 3,
column_of_sample = "ID",
adjust_eset = FALSE
)
pdata |
phenotype data of input sample; if phenotype data is NULL, create a data frame with 'Index' and 'ID' contain column names of eset |
eset |
normalized transcriptomic data: normalized (CPM, TPM, RPKM, FPKM, etc.), Gene expression data should be scale before signature score estimation |
signature |
List of gene signatures; |
mini_gene_count |
filter out signatures with genes less than minimal gene in expression set |
column_of_sample |
Defines in which column of pdata the sample identifier can be found. |
adjust_eset |
remove variables with missing value, sd =0, and Inf value |
signature scores for gene sets; signatures in columns, samples in rows
Dongqiang Zeng
# Loading TCGA-STAD expresion data(raw count matrix)
data("eset_stad", package = "IOBR")
# transform count data to tpm
eset <- count2tpm(eset_stad, idType = "ensembl")
# signature score estimation using PCA method
calculate_sig_score_pca(eset = eset, signature = signature_tme)
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