IOComMA: IO functions in 'ComMA'
In walterxie/ComMA: Community Matrix Analysis

Description Usage Arguments Details Examples

IO functions for the data defined in ComMA package, such as community matrix.

readCommunityMatrix(file, matrix.name = NULL, minAbund = 2,
  regex1 = "(\\|[0-9]+)", regex2 = "", ignore.case = TRUE,
  col.name.decreasing = FALSE, verbose = TRUE)

writeCommunityMatrix(community.matrix, file, msg.file = "file",
  msg.col = "columns", msg.row = "rows", regex1 = NULL, regex2 = "",
  ignore.case = TRUE)

readTaxaTable(file, matrix.name = NULL, taxa.group = "assigned",
  rank = "kingdom", regex1 = "(\\|[0-9]+)", regex2 = "",
  ignore.case = TRUE, include = TRUE, sep = "\t", verbose = TRUE)

createTaxaTableMEGAN(folder.path, file.prefix, sep = "\t",
  regex1 = "(\\|[0-9]+)", regex2 = "", ignore.case = TRUE,
  col.names = c("path", "kingdom", "phylum", "class", "order", "family",
  "genus"), file.out = "taxa-table-megan.txt")

createTaxaTableRDP(file, sep = "\t", rm.rank.prefix = TRUE,
  regex1 = "(\\|[0-9]+)", regex2 = "", ignore.case = TRUE,
  file.out = "taxa-table-rdp.txt")

`file`	The file to read/write.
`matrix.name`	The string to locate the matrix from its file name.
`minAbund`	The minimum abundance threshold to remove rows/columns by row/column sum of abundance. For exampe, if minAbund=2, then remove all singletons appeared in only one sample. If minAbund=1, then remove all empty rows/columns. Default to 2 (singletons). But `postfix` is only used for naming, no data processed.
`regex1, regex2`	Use for `gsub(regex1, regex2, row.names)` to remove or replace annotation from original labels. Default to `regex1="(\\|[0-9]+)", regex2=""` for read??? but NULL to write???, which removes size annotation seperated by "\|".
`ignore.case`	Refer to `gsub`.
`col.name.decreasing`	Should the sort decreasing order of `colnames` be TRUE? Refer to `order`. If NULL, do nothing. Default to FALSE.
`taxa.group`	The taxonomic group, the values can be 'all', 'assigned', or Group 'all' includes everything. Group 'assigned' removes all uncertain classifications including 'root', 'cellular organisms', 'No hits', 'Not assigned'. Alternatively, any high-ranking taxonomy in your taxonomy file can be used as a group or multi-groups (seperated by "\|"), such as 'BACTERIA', 'Proteobacteria', etc. But they have to be in the same rank column in the file. Default to remove all uncertain classifications, even when group(s) assigned.
`rank`	The rank column in the file to specify where to search for `taxa.group`.
`include`	Define whether include or exclude given `taxa.group`. Default to TRUE.
`folder.path`	The folder path to contain taxa mapping files and output MEGAN taxa table.
`file.prefix`	The prefix to find taxa mapping files, such as "16s" for "16s-path.txt", "16s-kingdom.txt", "16s-phylum.txt".
`col.names`	A vector of column names of taxonomic ranks in the taxa table, and they also determine the files to be merged into columns. Default to c("path", "kingdom", "phylum", "class", "order", "family", "genus"), which indicates the list of files c("16s-path.txt", "16s-kingdom.txt", "16s-phylum.txt", "16s-class.txt", "16s-order.txt", "16s-family.txt", "16s-genus.txt") given file.prefix = "16s". "path" is optional.
`file.out`	The taxonomic table file name.
`rm.rank.prefix`	Remove rank prefix, such as 'k__'. Default to TRUE.

readCommunityMatrix reads file to return a community matrix.

writeCommunityMatrix writes a community matrix to file.

readTaxaTable reads a file to return a taxa table. subsetTaxaTable can be used to takes or excludes a subset of the taxa table recursively.

createTaxaTableMEGAN reads a list of taxa mapping files exported from MEGAN to create a taxa table in folder.path.

createTaxaTableRDP reads a 3-column taxa mapping file generated from RDP to create a taxa table in folder.path. The row look like: OTU1 k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__ 0.970

cm <- readCommunityMatrix("16S.txt", "16S")

writeCommunityMatrix(cm, "16S-new.txt", msg.file="16S")

tt.megan <- readTaxaTable("16s-megan.txt", "16S taxa table", taxa.group="Bacteria")
tt.rdp.8 <- readTaxaTable("16s-rdp.txt", "16S taxa table", taxa.group="Bacteria")

createTaxaTableMEGAN(getwd(), "16s", file.out="16s-megan.txt")

createTaxaTableRDP("otus_tax_assignments.txt", file.out="16s-rdp.txt")