ic_score: ic_score

In oriolarques/GEGVIC: A workflow to analyse Gene Expression, Genetic Variations and Immune cell Composition of tumour samples using Next Generation Sequencing data.

ic_score

Description

Calculates and plots immunophenogram (IPG) and immunophenoscores (IPS) for each sample and each group of study.

Usage

ic_score(
  tpm,
  metadata,
  response,
  compare = NULL,
  p_label = "p.format",
  colors = c("orange", "black")
)

Arguments

tpm	Output from the ic_raw_to_tpm function. This is a matrix containing expression counts as TPM with HGNC gene symbols as rownames and samples identifiers as colnames.
metadata	Data frame that contains supporting variables to the data.
response	Unquoted name of the variable indicating the groups to analyse.
compare	A character string indicating which method to be used for comparing means. Options are 't.test' and 'wilcox.test' for two groups or 'anova' and 'kruskal.test' for more groups. Default value is NULL.
p_label	Character string specifying label type. Allowed values include 'p.signif' (shows the significance levels), 'p.format' (shows the formatted p-value).
colors	Character vector indicating the colors of the different groups to compare. Default values are two: black and orange.

Value

Returns ggplot objects and a data frame.

Examples

tpm <- ic_raw_to_tpm(counts = sample_counts,
                     genes_id = 'entrezgene_id',
                     biomart = ensembl_biomart_GRCh38_p13)
ips <- ic_score(tpm = tpm,
                metadata = sample_metadata,
                response = MSI_status,
                compare = 'wilcox.test',
                p_label = 'p.format',
                colors = c('orange', 'black'))

oriolarques/GEGVIC documentation built on Oct. 30, 2024, 10:44 p.m.