getLabels             package:maigesPack             R Documentation

_M_e_t_h_o_d _g_e_t_L_a_b_e_l_s _t_o _p_i_c_k _g_e_n_e _a_n_d _s_a_m_p_l_e _l_a_b_e_l_s

_D_e_s_c_r_i_p_t_i_o_n:

     Generic function 'getLabels' to extract labels given an ID to
     genes or samples.

_U_s_a_g_e:

     getLabels(obj, labelID=NULL, sLabel=TRUE)

     ## Default S3 method:
     getLabels(obj=NULL, labelID=NULL, sLabel=TRUE)

     ## S3 method for class 'maigesDE':
     getLabels(obj=NULL, labelID=NULL, sLabel=TRUE)

     ## S3 method for class 'maigesDEcluster':
     getLabels(obj=NULL, labelID=NULL, sLabel=TRUE)

     ## S3 method for class 'RGList':
     getLabels(obj=NULL, labelID=NULL, sLabel=TRUE)

     ## S3 method for class 'MAList':
     getLabels(obj=NULL, labelID=NULL, sLabel=TRUE)

     ## S3 method for class 'marrayRaw':
     getLabels(obj=NULL, labelID=NULL, sLabel=TRUE)

     ## S3 method for class 'marrayNorm':
     getLabels(obj=NULL, labelID=NULL, sLabel=TRUE)

_A_r_g_u_m_e_n_t_s:

     obj: object to look for labels. Methods defined for classes
          'maigesRaw', 'maiges', 'maigesDE', 'maigesDEcluster',
          'RGList', 'MAList', 'marrayRaw' and 'marrayNorm'.

 labelID: character string with label name to be searched.

  sLabel: logical indicating search in the sample labels, defaults to
          TRUE. If FALSE search is done for gene labels.

_D_e_t_a_i_l_s:

     The name of gene labels are done by the names of the slot
     'Glabels' in objects of classes 'maigesRaw' or 'maiges', the slot
     'GeneInfo' in objects of classes 'maigesDE' or 'maigesDEcluster',
     the slot 'genes' in objects of classes 'RGList' or 'MAList' and
     the slot 'maGnames@maInfo' in objects of classes 'marrayRaw' or
     'marrayNorm'. Equivalently, the name of sample labels are done by
     the names of the slots 'Slabels', 'SampleInfo', 'targets' and
     'maTargets@maInfo'.

_A_u_t_h_o_r(_s):

     Gustavo H. Esteves <gesteves@vision.ime.usp.br>

_E_x_a_m_p_l_e_s:

     ## Loading dataset
     data(gastro)

     ## Getting the 'Tissue' label for samples in maigesRaw class object
     getLabels(gastro.raw, "Tissue", sLabel=TRUE)

     ## Getting the 'Type' label for samples in maigesNorm class object
     getLabels(gastro.summ, "Type", sLabel=TRUE)

     ## Getting the 'GeneName' label for genes (spots) in maigesRaw class object
     getLabels(gastro.raw, "GeneName", sLabel=FALSE)

     ## Getting the 'Annot' label for samples in maigesNorm class object
     getLabels(gastro.summ, "Annot", sLabel=FALSE)

