write_report: Write a report
In xyomics/bugpower: Generate power calculation report for microbiome data

Description Usage Arguments Details Value Author(s)

View source: R/report.R

write_report Write a report

write_report(outputdir, filename, author,
  title = "Power calculation report for microbiome data",
  datatype = c("species", "metagenomics_pathways",
  "metatranscriptomics_pathways"), N_sample = c(200, 200, 200),
  N_feature = c(300, 300, 300), N_covariate = c(5, 5, 5), N_repeat = c(1,
  1, 1), contin = c(TRUE, TRUE, TRUE), conti_prop = c(0.5, 0.5, 0.5),
  pos_prop = c(0.2, 0.2, 0.2), increment = 0.005, q_cutoff = 0.05,
  target_power = 0.9, target_fpr = 0.05,
  mean_distribution_bugs = ref_dat$mean_distribution_bugs,
  mean_distribution_pathway_dna = ref_dat$mean_distribution_pathway_dna,
  mean_distribution_pathway_rna = ref_dat$mean_distribution_pathway_rna,
  sd_quartile_bugs_common = ref_dat$sd_quartile_bugs[1, ],
  sd_quartile_bugs_rare = ref_dat$sd_quartile_bugs[2, ],
  sd_quartile_pathway_dna_common = ref_dat$sd_quartile_pathway_dna[1, ],
  sd_quartile_pathway_dna_rare = ref_dat$sd_quartile_pathway_dna[2, ],
  sd_quartile_pathway_rna_common = ref_dat$sd_quartile_pathway_rna[1, ],
  sd_quartile_pathway_rna_rare = ref_dat$sd_quartile_pathway_rna[2, ],
  source = c("STAR project", "STAR project", "STAR project"))

`outputdir`	Output directory of the report. String. Default is current working directory.
`filename`	Filename of the report. String. Default is "report".
`author`	Author of the report. String. Default is "".
`title`	Title of the report. String. Default is "Power calculation report for microbiome data".
`datatype`	Data type needed in the report. Vector. Default is c("species", "metagenomics_pathways","metatranscriptomics_pathways").
`N_sample`	Number of samples in each data set. Vector. Default is c(200,200,200).
`N_feature`	Number of features in each data set. Vector. Default is c(300,300,300).
`N_covariate`	Number of covariates in the study. Number. Default is 5.
`N_repeat`	Number of repeat measurements for each data set. Vector. Default is c(2,2,2).
`contin`	The type of covariate we are interested. The type includeds "continous", "discrete" and "inter" (interaction). Strint. Default is c("continuous","continuous","continuous").
`pos_prop`	The proportion of features correlated with the variable we are interested in. Vector. Default is c(0.2,0.2,0.2)
`increment`	A small number to adjust the smoothness of the power curve. The smaller, the more smooth. Default is 0.005.
`q_cutoff`	The threshold for q value (p value after BH adjustment). A number in (0,1). Default is 0.05.
`target_power`	The least power the study wants to reach. A number in (0,1). Default is 0.9.
`target_fpr`	The highest false positive rate of the study. A number in (0,1). Default is 0.05.
`contin_prop`	The proportion of continuous covariates. Vector. Default is c(0.5,0.5,0.5)