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R CMD BUILD
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* checking for file funOmics/DESCRIPTION ... OK
* preparing funOmics:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building funomics_vignette.Rmd using rmarkdown
get_kegg_sets package:funOmics R Documentation
_R_e_t_r_i_e_v_e_s _K_E_G_G _p_a_t_h_w_a_y _g_e_n_e _s_e_t_s _f_o_r _a _s_p_e_c_i_f_i_e_d _o_r_g_a_n_i_s_m _a_n_d _g_e_n_e _I_D
_t_y_p_e.
_D_e_s_c_r_i_p_t_i_o_n:
This function retrieves KEGG pathway gene sets for a specified
organism. It fetches all pathways available for the specified
organism from the KEGG database and maps the genes involved in
each pathway. Currently, the function only supports choice of
gene identifiers (entrez IDs, gene symbols or Ensembl IDs) for
Homo sapiens (organism = "hsa") using the org.Hs.eg.db package.
_U_s_a_g_e:
get_kegg_sets(organism = "hsa", geneid_type = "entrez")
_A_r_g_u_m_e_n_t_s:
organism: The organism abbreviation for which KEGG pathway gene sets
are to be retrieved (e.g., "ecj" for E. coli). Default is
"hsa" (Homo sapiens).
geneid_type: The type of gene IDs to provide. Default is "entrez";
options are "entrez", "symbol", or "ensembl". This parameter
is only used when the organism is "hsa" (Homo sapiens).
_V_a_l_u_e:
A list where each element represents a KEGG pathway gene set. The
names of the list correspond to the pathway names.
_S_e_e _A_l_s_o:
'summarize_pathway_level'
'keggLink', 'keggList'
'mapIds'
_E_x_a_m_p_l_e_s:
# Retrieve KEGG pathway gene sets for Homo sapiens with entrez IDs (default)
hsa_kegg_sets_entrez <- get_kegg_sets()
# Retrieve KEGG molecular sets using gene symbols
hsa_kegg_sets_symbol <- get_kegg_sets(geneid_type = "symbol")
# Retrieve KEGG molecular sets using Ensembl IDs
hsa_kegg_sets_ensembl <- get_kegg_sets(geneid_type = "ensembl")
# Retrieve KEGG pathway gene sets for another organism (e.g., Escherichia coli)
ecoli_kegg_sets <- get_kegg_sets(organism = "ecj")
short_sets_detail package:funOmics R Documentation
_R_e_t_r_i_e_v_e _d_e_t_a_i_l_s _a_n_d _i_n_f_o_r_m_a_t_i_o_n _a_b_o_u_t _s_h_o_r_t _m_o_l_e_c_u_l_a_r _s_e_t_s
_D_e_s_c_r_i_p_t_i_o_n:
This function identifies molecular sets with sizes less than a
specified threshold and returns information about these sets.
_U_s_a_g_e:
short_sets_detail(sets, minsize)
_A_r_g_u_m_e_n_t_s:
sets: A list of molecular sets.
minsize: The minimum size threshold for sets.
_D_e_t_a_i_l_s:
This function identifies molecular sets in the input list that
have sizes less than the specified minimum size ('minsize'). It
returns a list containing the names, lengths, and molecules of
these short molecular sets.
_V_a_l_u_e:
A list containing information about short molecular sets:
short_sets: Names of the short molecular sets.
lengths: Lengths of the short molecular sets.
genes: Short molecular sets themselves.
_E_x_a_m_p_l_e_s:
ex_sets <- list(set1 = c("mol1", "mol2"), set2 = c("mol3", "mol4", "mol5"))
short_sets_info <- short_sets_detail(ex_sets, minsize = 3)
summarize_pathway_level package:funOmics R Documentation
_A_g_g_r_e_g_a_t_e_s _o_r _s_u_m_m_a_r_i_z_e_s _o_m_i_c_s _d_a_t_a _i_n_t_o _h_i_g_h_e_r-_l_e_v_e_l _f_u_n_c_t_i_o_n_a_l
_r_e_p_r_e_s_e_n_t_a_t_i_o_n_s _t_h_a_t _c_a_n _b_e _i_n_t_e_r_p_r_e_t_e_d _a_s _f_u_n_c_t_i_o_n_a_l _a_c_t_i_v_i_t_y _s_c_o_r_e_s
_o_r _m_e_a_s_u_r_e_s.
_D_e_s_c_r_i_p_t_i_o_n:
Given an omics matrix and a list of functional molecular sets,
this function aggregates or summarizes the omics data into
higher-level functional representations such as GO terms gene sets
or KEGG metabolic pathways, facilitating the analysis of
functional molecular sets that allow reducing dimensionality and
providing easier and faster biological interpretations.
Coordinated functional activity scores can be as informative as
single molecules.
_U_s_a_g_e:
summarize_pathway_level(omicsmat, sets = NULL, type = "mean", minsize = 10)
_A_r_g_u_m_e_n_t_s:
omicsmat: A matrix or data frame representing omics data. Rows
correspond to molecular identifiers, and columns correspond
to samples.
sets: A list of functional sets. Each element in the list should
represent a molecular set, and the elements of the set should
match the row names of the omics matrix.
type: The type of pooling operator to be applied for each set.
Possible values include "mean" (default), "median", "sd",
"min", "max", "pca", "mds", "pathifier", "nmf", "ttest",
"wilcox", "kolmogorov".
minsize: The minimum size per molecular set (default is 10).
_D_e_t_a_i_l_s:
Notes:
- Different aggregation operators can be used, including summary
statistics such as median (default), mean, sd, min, max,
dimensionality reduction scores such as pca, mds, pathifier, or
nmf, and statistical tests such as ttest, wilcoxon test,
kolmogorov test.
- The minimum size per molecular set is by default 10 molecules
(e.g. genes or metabolites) and can be changed with the parameter
minsize.
- If "pathifier" is chosen as pooling type, the `aggby_pathifier`
function internally generates a log file named 'pathifierlog.txt'
during its execution.
This log file may contain additional information that could be
useful for troubleshooting or advanced analysis.
Users typically do not need to interact with this file directly,
but it is mentioned here for informational purposes. For more
details, this function utilizes the Pathifier package.
_V_a_l_u_e:
A matrix-like table with the activity measures for each group or
set of molecules, i.e., sxn matrix, for s molecular sets and n
samples.
_A_u_t_h_o_r(_s):
Elisa Gomez de Lope
_E_x_a_m_p_l_e_s:
# Example usage:
g <- 10000
s <- 20
X <- matrix(abs(rnorm(g * s)), nrow = g, dimnames = list(paste0("g", 1:g), paste0("s", 1:s)))
pathways <- as.list(sample(10:100, size = 100, replace = TRUE))
pathways <- lapply(pathways, function(s, g) paste0("g", sample(1:g, size = s, replace = FALSE)), g)
names(pathways) <- paste0("pathway", seq_along(pathways))
pathway_activity <- summarize_pathway_level(X, pathways, type = "mean", minsize = 12)
Quitting from lines at lines 182-184 [unnamed-chunk-18] (funomics_vignette.Rmd)
Error: processing vignette 'funomics_vignette.Rmd' failed with diagnostics:
'what' must be a function or character string
--- failed re-building funomics_vignette.Rmd
SUMMARY: processing the following file failed:
funomics_vignette.Rmd
Error: Vignette re-building failed.
Execution halted