dbGetGeneRegulationRanking       package:maDB       R Documentation

_R_a_n_k _g_e_n_e_s _a_c_c_o_r_d_i_n_g _t_o _t_h_e _n_u_m_b_e_r _o_f _c_o_m_p_a_r_i_s_o_n_s _t_h_e_y _a_r_e _r_e_g_u_l_a_t_e_d.

_D_e_s_c_r_i_p_t_i_o_n:

     This function can be used to generate a ranking list for genes
     that contains the number of comparisons (from a selected set of
     comparisons in the database) the gene was regulated (where
     regulation can be for example be defined as an M value bigger than
     1 or smaller -1). The ranking can be restricted to a subset of
     genes and comparisons. Note that the comparisons have to be
     created in the database (from expresison values using the
     'dbCalculateRegulations' method). By default the function maps
     first the submitted ids to UniGene IDs and calcultates therefore
     the ranking for genes (not for, in the case of Affymetrix, probe
     sets), bevertheless by setting 'no.mapping.to.ug=TRUE' this
     mapping to UniGene IDs will be skipped and the ranking will be
     performed id per id.

_U_s_a_g_e:

     dbGetGeneRegulationRanking(con, ug = NULL, id = NULL, include.by.name = NULL, exclude.by.name = NULL, include.by.pk = NULL, exclude.by.pk = NULL, count.cols = NULL, write.info.file = TRUE, search.column = "exposure_time", no.mapping.to.ug = FALSE ,m.up= 1, m.down= -1, v = TRUE, chip=NULL)

_A_r_g_u_m_e_n_t_s:

     con: The connection to the (maDB) database.

      ug: A set of UniGene identifiers. The annotation table has to be
          created if this option is used!

      id: A set of ids (eg Affymetrix probe set IDs or the IDs that
          were used as rownames in the 'EexprSet@exprs' tables that
          were inserted into the database).

include.by.name: The comparisons are joined to the samples table. So
          comparisons can be selected or using the 'include.by.pk'
          attribute, or using the sample names of the samples that were
          used as \textit{red} signal channels in the calculation of
          the regulation value ('M = log2(R / G)').

exclude.by.name: Samples that should be excluded.

include.by.pk: The primary keys of the comparisons that should be
          included to create the ranking.

exclude.by.pk: The primary keys of the comparisons that should be
          excluded (makes only sense when the 'include.by.name' was
          used, and not all of the comparisons that share the same
          sample names should be included).

count.cols: The entries (of the samples table) that should be used to
          count the regulation. For example if you have in your
          database samples with 6 hours, 8 hours and 24 hours exposure
          time and you want to count for each gene the number of
          comparisons with 6 and 8 hours where they were regulated and
          additionally the number of comparisons with 24 hours exposure
          time samples, submit 'count.cols=list(c("6h","8h"),c("24h"))'
          and for the attribute search.col
          'search.col="exposure_time"'.

write.info.file: If true a file called "HL" with the current date and
          "Info.txt" will be saved in the current working directory
          which contains the information which comaprisons were used to
          generate the ranking.

search.column: The column of the samples table that should be used to
          distinguish between different comparisons (see attribute
          count.cols).

no.mapping.to.ug: If TRUE the ranking will be computed for each
          submitted id, if FALSE each id will be mapped to UniGene IDs,
          and those will then be used to count the regulations. Because
          of this mapping it is important, that the annotation table in
          the database holds the correct information (see
          'dbUpdateAnnotation' for more information).

    m.up: Genes that have an M value bigger than this value will be
          counted as regulated (up-regulated!), the default is 1.

  m.down: Genes that have an M value smaller than this value will be
          counted as down-regulated.

       v: If additional information (progress bar...) should be written
          to the console.

    chip: The chip or array type (eg hgu133plus2).

_D_e_t_a_i_l_s:

     coming soon...

_V_a_l_u_e:

     A table with the information about how many times a gene was
     regulated.

_A_u_t_h_o_r(_s):

     Johannes Rainer

_S_e_e _A_l_s_o:

     'dbUpdateAnnotation', 'publishToDB', 'dbCalculateRegulations'

