Man pages for jdreyf/ezlimma
Streamlines and extends limma package

add_zcolsAdd column to toptab with z-stats
batch2designTransform factor vector into design matrix
clean_filenamesAlter names to valid filenames
combine_pvaluesCombine p-values of a feature over multiple p-value columns...
df_signifApply 'signif' function to numeric columns of data frames
ezcameraprA wrapper function for 'cameraPR' with output to Excel
ezcorTest correlation of each row of an object to a phenotype...
ezebayesWrapper for limma's eBayes function that also allows for...
eztoptabWrapper for limma topTable function
fc2ratioTransform fold-change (FC) into a ratio
fisher_enrichmentFisher Exact Test of gene set enrichment with output to Excel
g_indexCreate object with indices of genes per gene set
gmat2gmtTransform analyte-by-pathway matrix into list compatible with...
grep_colsFind p-value or stat columns in table
grp_meansCalculate group means per feature
limma_contrastsApply limma's lmFit, contrasts.fit, & eBayes to one or more...
limma_corTest correlation of each row of object to phenotype using...
limma_tostTwo one-sided test procedure with 'limma' for statistical...
logfc2fcTransform a log2 fold-change to a fold-change
map_glistMap pathway list gene IDs to another ID type
multi_corTest correlation of each row of an object to each column of...
multi_fisher_enrichmentFisher Exact Test of gene set enrichment with multiple...
multiTopTabCombine one or more toptables extracted from linear model fit
prop_changedCalculate proportion of changed features per pathway
read_gmtRead gene set file with GMT extension to a list
read_linked_xlRead Excel XLSX file with links to CSVs
roast_contrastsTest contrasts of gene sets between groups using rotation...
roast_corto Excel
roast_multi_corto Excel
roast_two2one_tailedConvert roast two-tailed results to one-tailed
sim_fisherApply 'fisher_enrichment' to simulated data
SMPDB2GTransform SMPDB protein and/or metabolite pathway data frames...
two2one_tailedConvert 2-tailed into 1-tailed p-values
write_gmtWrite gene set file with GMT extension from a list
write_linked_xlWrite Excel XLSX file with links to CSVs
xl_pwysMake XL data frame for 'writexl'
jdreyf/ezlimma documentation built on March 3, 2024, 4:23 a.m.