In goodarzilab/APAlog: Analysis of alternative poly A site usage

APAlog Tutorial

library('APAlog')

Load Counts Matrix and Design

pA.toy2 <- APAlog::pA.toy2
pA_design <- APAlog::pA_design

head(pA.toy2)

head(pA_design)

Transcript-wise Testing

fit.o_HNRNPC_fdr <- APAlog::pA_logit_dev(pA.toy2,
                                         pA.site ~ cell_line,
                                         pA_design,
                                         "sample",  
                                         adj_method = "fdr")

head(fit.o_HNRNPC_fdr)

Pairwise Testing

fit.p_HNRNPC <- APAlog::pA_logit_pairwise(pA.toy2, pA.site~cell_line, pA_design, "sample")

fit.op_HNRNPC <- merge(fit.o_HNRNPC_fdr, fit.p_HNRNPC, by = "transcript")

head(fit.op_HNRNPC)

• Volcano Plot for the corrected p-values against the log fold change

APAlog::volcano_plot(fit.op_HNRNPC,
                     x='b_cell_lineMDA_sgHNRNPC',
                     y='p_cell_lineMDA_sgHNRNPC',
                     title='Volcano plot for the toy dataset',
                     pCutoff = 0.05,
                     FCcutoff = 1,
                     ylim=c(0,2))

Multinomial Testing

fit.m_HNRNPC_fdr <- pA_multi_logit(pA.toy2,
                                   pA.site ~ cell_line,
                                   pA_design,
                                   "sample",
                                   adj_method='fdr')

head(fit.m_HNRNPC_fdr)

• Volcano Plot for the corrected p-values against the log fold change

APAlog::volcano_plot(fit.m_HNRNPC_fdr,
                     x='b_cell_lineMDA_sgHNRNPC',
                     y='p_cell_lineMDA_sgHNRNPC',
                     title='Volcano plot for the toy dataset',
                     pCutoff = 0.05,
                     FCcutoff = 1,
                     ylim=c(0,2))

goodarzilab/APAlog documentation built on March 25, 2022, 3:40 p.m.